Mass spectrometer

ABSTRACT

A mass spectrometer is disclosed comprising an ion mobility spectrometer or separator and an ion guide arranged downstream of the ion mobility spectrometer or separator. A plurality of axial potential wells are created in the ion guide so that ions received from the ion mobility spectrometer or separator become confined in separate axial potential wells. The potential wells maintain the fidelity and/or composition of ions received from the ion mobility spectrometer or separator. The potential wells are translated along the length of the ion guide.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.15/231,045, filed Aug. 8, 2016, which is a continuation of U.S. patentapplication Ser. No. 14/725,451, filed on May 29, 2015, now U.S. Pat.No. 9,410,927 which is continuation of U.S. patent application Ser. No.14/256,301, filed on Apr. 18, 2014, now U.S. Pat. No. 9,048,073, whichis a continuation of U.S. patent application Ser. No. 14/064,616, filedon Oct. 28, 2013, now U.S. Pat. No. 8,735,805, which is a continuationof U.S. patent application Ser. No. 13/663,191, filed on Oct. 29, 2012,now U.S. Pat. No. 8,569,687, which is a continuation of U.S. patentapplication Ser. No. 12/917,720, filed on Nov. 2, 2010, now U.S. Pat.No. 8,299,422, which is a continuation of U.S. patent application Ser.No. 11/718,213, filed Jul. 23, 2007, now U.S. Pat. No. 7,829,841, whichis the National Stage of International Application No.PCT/GB2005/004238, filed on Nov. 3, 2005, which claims priority to andbenefit of U.S. Provisional Patent Application Ser. No. 60/628,215,filed on Nov. 16, 2004, and priority to and benefit of United KingdomPatent Application No. 0424426.5, filed Nov. 4, 2004. The entirecontents of these applications are incorporated herein by reference.

BACKGROUND OF THE INVENTION

The present invention relates to a mass spectrometer and a method ofmass spectrometry.

With the decoding of the 20-30,000 genes that compose the human genome,emphasis has switched to the identification of the translated geneproducts that comprise the proteome. Mass spectrometry has firmlyestablished itself as the primary technique for identifying proteins dueto its unparalleled speed, sensitivity and specificity. Strategies caninvolve either analysis of the intact protein or more commonly digestionof the protein using a specific protease that cleaves at predictableresidues along the peptide backbone. This provides smaller stretches ofpeptide sequence that are more amenable to analysis via massspectrometry.

A mass spectrometer comprising an Electrospray Ionisation (“ESI”) ionsource interfaced to a tandem mass spectrometer has a particularly highdegree of specificity and sensitivity. A complex digest mixture may beseparated by microcapillary liquid chromatography with on-line massspectral detection using automated acquisition modes whereby MS andMS/MS spectra may be collected in a data dependent manner. Thisinformation may then be used to search databases directly for matchingsequences. This may lead to identification of the parent proteinespecially if the protein is present at low endogenous concentrations.However, often the limiting factor for identification of a protein isnot the quality of the MS/MS mass spectrum produced, but rather is theinitial recognition of multiply charged peptide parent or precursor ionsin the MS mode. This is often due to the relatively high level oflargely singly charged background ions emitted by the ion source andwhich appear in the resulting mass spectrum.

It would therefore be desirable to be able to recognise more easilymultiply charged analyte ions of interest which are present in a mixtureof ions which may comprise a significant proportion of singly chargedbackground ions.

SUMMARY OF THE INVENTION

According to a first aspect of the present invention there is provided amass spectrometer comprising:

an ion mobility spectrometer or separator;

a first ion guide arranged downstream of the ion mobility separator orspectrometer, the first ion guide being arranged to receive ions fromthe ion mobility spectrometer or separator, and wherein the first ionguide comprises a plurality of electrodes;

a first voltage means arranged and adapted to apply one or more voltagesor one or more voltage waveforms to the plurality of electrodes so thatin a first mode of operation ions received from the ion mobilityspectrometer or separator are retained and/or confined and/ortransported and/or translated in separate regions or portions of thefirst ion guide; and

a mass analyser arranged downstream of the first ion guide.

The ion mobility spectrometer or separator preferably comprises a gasphase electrophoresis device. According to a preferred embodiment theion mobility spectrometer or separator may comprise: (i) a drift tube;(ii) a multipole rod set; (iii) an ion tunnel or ion funnel; or (iv) astack or array of planar, plate or mesh electrodes.

The drift tube preferably comprises one or more electrodes and means formaintaining an axial DC voltage gradient or a substantially constant orlinear axial DC voltage gradient along at least 5%, 10%, 15%, 20%, 25%,30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or100% of the axial length of the drift tube.

The multipole rod set preferably comprises a quadrupole rod set, ahexapole rod set, an octapole rod set or a rod set comprising more thaneight rods.

The ion tunnel or ion funnel preferably comprises a plurality ofelectrodes or at least 2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100electrodes having apertures through which ions are transmitted in use,wherein at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%,60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the electrodes haveapertures which are of substantially the same size or area or which haveapertures which become progressively larger and/or smaller in size or inarea. According to a preferred embodiment at least 5%, 10%, 15%, 20%,25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,95% or 100% of the electrodes have internal diameters or dimensionsselected from the group consisting of: (i) ≥1.0 mm; (ii) ≤2.0 mm; (iii)≤3.0 mm; (iv) ≤4.0 mm; (v) ≤5.0 mm; (vi) ≤6.0 mm; (vii) ≤7.0 mm; (viii)≤8.0 mm; (ix) ≤9.0 mm; (x) ≤10.0 mm; and (xi) >10.0 mm.

The stack or array of planar, plate or mesh electrodes preferablycomprises a plurality or at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20 planar, plate or mesh electrodes whereinat least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%,70%, 75%, 80%, 85%, 90%, 95% or 100% of the planar, plate or meshelectrodes are arranged generally in the plane in which ions travel inuse. According to a preferred embodiment at least some or at least 5%,10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%,80%, 85%, 90%, 95% or 100% of the planar, plate or mesh electrodes aresupplied with an AC or RF voltage and wherein adjacent planar, plate ormesh electrodes are supplied with opposite phases of the AC or RFvoltage.

According to a preferred embodiment the ion mobility spectrometer orseparator preferably comprises a plurality of axial segments or at least5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90,95 or 100 axial segments.

According to an embodiment the mass spectrometer preferably furthercomprises DC voltage means for maintaining a substantially constant DCvoltage gradient along at least a portion or at least 5%, 10%, 15%, 20%,25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,95% or 100% of the axial length of the ion mobility spectrometer orseparator in order to urge at least some ions along at least a portionor at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%,65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the axial length of the ionmobility spectrometer or separator.

According to an embodiment the mass spectrometer preferably comprisestransient DC voltage means arranged and adapted to apply one or moretransient DC voltages or potentials or one or more transient DC voltageor potential waveforms to electrodes forming the ion mobilityspectrometer or separator in order to urge at least some ions along atleast 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%,70%, 75%, 80%, 85%, 90%, 95% or 100% of the axial length of the ionmobility spectrometer or separator.

According to an embodiment the mass spectrometer preferably comprises ACor RF voltage means arranged and adapted to apply two or morephase-shifted AC or RE voltages to electrodes forming the ion mobilityspectrometer or separator in order to urge at least some ions along atleast 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%,70%, 75%, 80%, 85%, 90%, 95% or 100% of the axial length of the ionmobility spectrometer or separator.

The ion mobility spectrometer or separator preferably has an axiallength selected from the group consisting of: (i) <20 mm; (ii) 20-40 mm;(iii) 40-60 mm; (iv) 60-80 mm; (v) 80-100 mm; (vi) 100-120 mm; (vii)120-140 mm; (viii) 140-160 mm; (ix) 160-180 mm; (x) 180-200 mm; (xi)200-220 mm; (xii) 220-240 mm; (xiii) 240-260 mm; (xiv) 260-280 mm; (xv)280-300 mm; (xvi) >300 mm.

According to a preferred embodiment the ion mobility spectrometer orseparator preferably further comprises AC or RF voltage means arrangedand adapted to apply an AC or RF voltage to at least 5%, 10%, 15%, 20%,25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,95% or 100% of the plurality of electrodes of the ion mobilityspectrometer or separator in order to confine ions radially within theion mobility spectrometer or separator. The AC or RF voltage means ispreferably arranged and adapted to supply an AC or RF voltage to theplurality of electrodes of the ion mobility spectrometer or separatorhaving an amplitude selected from the group consisting of: (i) <50 Vpeak to peak; (ii) 50-100 V peak to peak; (iii) 100-150 V peak to peak;(iv) 150-200 V peak to peak; (v) 200-250 V peak to peak; (vi) 250-300 Vpeak to peak; (vii) 300-350 V peak to peak; (viii) 350-400 V peak topeak; (ix) 400-450 V peak to peak; (x) 450-500 V peak to peak; and(xi) >500 V peak to peak. The AC or RF voltage means is preferablyarranged and adapted to supply an AC or RF voltage to the plurality ofelectrodes of the ion mobility spectrometer or separator having afrequency selected from the group consisting of: (i) <100 kHz; (ii)100-200 kHz; (iii) 200-300 kHz; (iv) 300-400 kHz; (v) 400-500 kHz; (vi)0.5-1.0 MHz; (vii) 1.0-1.5 MHz; (viii) 1.5-2.0 MHz; (ix) 2.0-2.5 MHz;(x) 2.5-3.0 MHz; (xi) 3.0-3.5 MHz; (xii) 3.5-4.0 MHz; (xiii) 4.0-4.5MHz; (xiv) 4.5-5.0 MHz; (xv) 5.0-5.5 MHz; (xvi) 5.5-6.0 MHz; (xvii)6.0-6.5 MHz; (xviii) 6.5-7.0 MHz; (xix) 7.0-7.5 MHz; (xx) 7.5-8.0 MHz;(xxi) 8.0-8.5 MHz; (xxii) 8.5-9.0 MHz; (xxiii) 9.0-9.5 MHz; (xxiv)9.5-10.0 MHz; and (xxv) >10.0 MHz.

According to a preferred embodiment singly charged ions having a mass tocharge ratio in the range of 0-100, 100-200, 200-300, 300-400, 400-500,500-600, 600-700, 700-800, 800-900 or 900-1000 preferably have a driftor transit time through the ion mobility spectrometer or separator inthe range: (i) 0-1 ms; (ii) 1-2 ms; (iii) 2-3 ms; (iv) 3-4 ms; (v) 4-5ms; (vi) 5-6 ms; (vii) 6-7 ms; (viii) 7-8 ms; (ix) 8-9 ms; (x) 9-10 ms;(xi) 10-11 ms; (xii) 11-12 ms; (xiii) 12-13 ms; (xiv) 13-14 ms; (xv)14-15 ms; (xvi) 15-16 ms; (xvii) 16-17 ms; (xviii) 17-18 ms; (xix) 18-19ms; (xx) 19-20 ms; (xxi) 20-21 ms; (xxii) 21-22 ms; (xxiii) 22-23 ms;(xxiv) 23-24 ms; (xxv) 24-25 ms; (xxvi) 25-26 ms; (xxvii) 26-27 ms;(xxviii) 27-28 ms; (xxix) 28-29 ms; (xxx) 29-30 ms; and (xxxi) >30 ms.

The mass spectrometer preferably further comprises means arranged andadapted to maintain at least a portion of the ion mobility spectrometeror separator at a pressure selected from the group consisting of:(i) >0.001 mbar; (ii) >0.01 mbar; (iii) >0.1 mbar; (iv) >1 mbar; (v) >10mbar; (vi) >100 mbar; (vii) 0.001-100 mbar; (viii) 0.01-10 mbar; and(ix) 0.1-1 mbar.

The mass spectrometer preferably further comprises means for introducinga first gas into the ion mobility spectrometer or separator, the firstgas being selected from or at least partially comprising a gas selectedfrom the group consisting of: (i) nitrogen; (ii) argon; (iii) helium;(iv) methane; (v) neon; (vi) xenon; and (vii) air.

According to a preferred embodiment the mass spectrometer preferablyfurther comprises a housing for the ion mobility spectrometer orseparator. The housing preferably forms a substantially gas tightenclosure apart from an ion entrance aperture, an ion exit aperture anda port for introducing a gas into the housing.

The mass spectrometer preferably further comprises means for pulsingions into the ion mobility spectrometer or separator once every 0-5 ms,5-10 ms, 10-15 ms, 15-20 ms, 20-25 ms, 25-30 ms, 30-35 ms, 35-40 ms,40-45 ms, 45-50 ms or >50 ins.

The first ion guide preferably comprises: (i) a multipole rod set or asegmented multipole rod set; (ii) an ion tunnel or ion funnel; or (iii)a stack or array of planar, plate or mesh electrodes.

According to an embodiment of the present invention a second ion guidemay be arranged upstream of the ion mobility spectrometer or separator.The second ion guide preferably comprises: (i) a multipole rod set or asegmented multipole rod set; (ii) an ion tunnel or ion funnel; or (iii)a stack or array of planar, plate or mesh electrodes.

The first and/or second ion guide may comprise a multipole rod setcomprising a quadrupole rod set, a hexapole rod set, an octapole rod setor a rod set comprising more than eight rods.

The first and/or second ion guide may comprise an ion tunnel or iontunnel comprises a plurality of electrodes or at least 2, 5, 10, 20, 30,40, 50, 60, 70, 80, 90 or 100 electrodes having apertures through whichions are transmitted in use, wherein at least 5%, 10%, 15%, 20%, 25%,30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or100% of the electrodes have apertures which are of substantially thesame size or area or which have apertures which become progressivelylarger and/or smaller in size or in area. Preferably, at least 5%, 10%,15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%,85%, 90%, 95% or 100% of the electrodes have internal diameters ordimensions selected from the group consisting of: (i) ≤1.0 mm; (ii) ≤2.0mm; (iii) ≤3.0 mm; (iv) ≤4.0 mm; (v) ≤5.0 mm; (vi) ≤6.0 mm; (vii) ≤7.0mm; (viii) ≤8.0 mm; (ix) ≤9.0 mm; (x) ≤10.0 mm; and (xi) >10.0 mm.

The first and/or second ion guides may comprise a stack or array ofplanar, plate or mesh electrodes preferably comprising a plurality or atleast 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or20 planar, plate or mesh electrodes arranged generally in the plane inwhich ions travel in use, wherein at least 5%, 10%, 15%, 20%, 25%, 30%,35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100%of the planar, plate or mesh electrodes are arranged generally in theplane in which ions travel in use. According to a preferred embodimentthe mass spectrometer preferably further comprises AC or RF voltagemeans for supplying the plurality of planar, plate or mesh electrodeswith an AC or RF voltage and wherein adjacent plate or mesh electrodesare supplied with opposite phases of the AC or RF voltage.

According to the preferred embodiment the first and/or second ion guidemay comprise a plurality of axial segments or at least 5, 10, 15, 20,25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100 axialsegments.

According to the preferred embodiment the mass spectrometer may furthercomprise transient DC voltage means arranged and adapted to apply one ormore transient DC voltages or potentials or one or more transient DCvoltage or potential waveforms to electrodes forming the first and/orsecond ion guides in order to urge at least some ions along at least 5%,10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%,80%, 85%, 90%, 95% or 100% of the axial length of the first and/orsecond ion guide.

According to the preferred embodiment the mass spectrometer maypreferably further comprise AC or RF voltage means arranged and adaptedto apply two or more phase-shifted AC or RF voltages to electrodesforming the first and/or second ion guide in order to urge at least someions along at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%,55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the axial lengthof the first and/or second ion guide.

The first and/or second ion guide preferably has an axial lengthselected from the group consisting of: (i) <20 mm; (ii) 20-40 mm; (iii)40-60 mm; (iv) 60-80 mm; (v) 80-100 mm; (vi) 100-120 mm; (vii) 120-140mm; (viii) 140-160 mm; (ix) 160-180 mm; (x) 180-200 mm; (xi) 200-220 mm;(xii) 220-240 mm; (xiii) 240-260 mm; (xiv) 260-280 mm; (xv) 280-300 mm;and (xvi) >300 mm.

The first and/or second ion guide preferably further comprises AC or RFvoltage means arranged and adapted to apply an AC or RF voltage to atleast 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%,70%, 75%, 80%, 85%, 90%, 95% or 100% of the plurality of electrodes ofthe first and/or second ion guide in order to confine ions radiallywithin the first and/or second ion guide. The AC or RF voltage means ispreferably arranged and adapted to supply an AC or RF voltage to theplurality of electrodes of the first and/or second ion guide having anamplitude selected from the group consisting of: (i) <50 V peak to peak;(ii) 50-100 V peak to peak; (iii) 100-150 V peak to peak; (iv) 150-200 Vpeak to peak; (v) 200-250 V peak to peak; (vi) 250-300 V peak to peak;(vii) 300-350 V peak to peak; (viii) 350-400 V peak to peak; (ix)400-450 V peak to peak; (x) 450-500 V peak to peak; and (xi) >500 V peakto peak. The AC or RF voltage means is preferably arranged and adaptedto supply an AC or RF voltage to the plurality of electrodes of thefirst and/or second ion guide having a frequency selected from the groupconsisting of: (i) <100 kHz; (ii) 100-200 kHz; (iii) 200-300 kHz; (iv)300-400 kHz; (v) 400-500 kHz; (vi) 0.5-1.0 MHz; (vii) 1.0-1.5 MHz;(viii) 1.5-2.0 MHz; (ix) 2.0-2.5 MHz; (x) 2.5-3.0 MHz; (xi) 3.0-3.5 MHz;(xii) 3.5-4.0 MHz; (xiii) 4.0-4.5 MHz; (xiv) 4.5-5.0 MHz; (xv) 5.0-5.5MHz; (xvi) 5.5-6.0 MHz; (xvii) 6.0-6.5 MHz; (xviii) 6.5-7.0 MHz; (xix)7.0-7.5 MHz; (xx) 7.5-8.0 MHz; (xxi) 8.0-8.5 MHz; (xxii) 8.5-9.0 MHz;(xxiii) 9.0-9.5 MHz; (xxiv) 9.5-10.0 MHz; and (xxv) >10.0 MHz.

According to the preferred embodiment singly charged ions having a massto charge ratio in the range of 1-100, 100-200, 200-300, 300-400,400-500, 500-600, 600-700, 700-800, 800-900 or 900-1000 preferably havea drift or transit time through the first and/or second ion guide in therange: (i) 0-10 μs; (ii) 10-20 μs; (iii) 20-30 μs; (iv) 30-40 μs; (v)40-50 μs; (vi) 50-60 μs; (vii) 60-70 μs; (viii) 70-80 μs; (ix) 80-90 μs;(x) 90-100 μs; (xi) 100-110 μs; (xii) 110-120 μs; (xiii) 120-130 μs;(xiv) 130-140 μs; (xv) 140-150 μs; (xvi) 150-160 μs; (xvii) 160-170 μs;(xviii) 170-180 μs; (xix) 180-190 μs; (xx) 190-200 μs; (xxi) 200-210 μs;(xxii) 210-220 μs; (xxiii) 220-230 μs; (xxiv) 230-240 μs; (xxv) 240-250μs; (xxvi) 250-260 μs; (xxvii) 260-270 μs; (xxviii) 270-280 μs; (xxix)280-290 μs; (xxx) 290-300 μs; and (xxxi) >300 μs.

According to the preferred embodiment the mass spectrometer preferablyfurther comprises means arranged and adapted to maintain at least aportion of the first and/or second ion guide at a pressure selected fromthe group consisting of: (i) >0.0001 mbar; (ii) >0.001 mbar; (iii) >0.01mbar; (iv) >0.1 mbar; (v) >1 mbar; (vi) >10 mbar; (vii) 0.0001-0.1 mbar;and (viii) 0.001-0.01 mbar.

The mass spectrometer preferably further comprises acceleration meansarranged and adapted to accelerate ions emerging from the ion mobilityspectrometer or separator into the first ion guide and wherein in asecond mode of operation at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%,45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of theions are caused to fragment upon entering the first ion guide. Theacceleration means is preferably arranged and adapted to progressivelyvary or increase the kinetic energy of ions emerging from the ionmobility spectrometer or separator as they are transmitted to the firstion guide. The acceleration means preferably comprises a region acrosswhich a potential difference is maintained and wherein the potentialdifference is progressively varied or increased with time.

The mass spectrometer preferably further comprises a control systemarranged and adapted to switch or repeatedly switch the potentialdifference through which ions pass prior to entering the first ion guidebetween a high fragmentation mode of operation wherein ions aresubstantially fragmented upon entering the first ion guide and a lowfragmentation mode of operation wherein substantially less ions arefragmented or wherein substantially no ions are fragmented upon enteringthe first ion guide.

In the high fragmentation mode of operation ions entering the first ionguide are preferably accelerated through a potential difference selectedfrom the group consisting of: (i) ≥10 V; (ii) ≥20 V; (iii) ≥30 V; (iv)≥40 V; (v) ≥50 V; (vi) ≥60 V; (vii) ≥70 V; (viii) ≥80 V; (ix) ≥90 V; (x)≥100 V; (xi) ≥110 V; (xii) ≥120 V; (xiii) ≥130 V; (xiv) ≥140 V; (xv)≥150 V; (xvi) ≥160 V; (xvii) ≥170 V; (xviii) ≥180 V; (xix) ≥190 V; and(xx) ≥200 V.

In the low fragmentation mode of operation ions entering the first ionguide are preferably accelerated through a potential difference selectedfrom the group consisting of: (i) ≤20 V; (ii) ≤15 V; (iii) ≤10 V; (iv)≤5V; and (v) ≤1V.

The control system is preferably arranged and adapted to switch thefirst ion guide between a high fragmentation mode of operation and a lowfragmentation mode of operation at least once every 1 ms, 5 ms, 10 ms,15 ms, 20 ms, 25 ms, 30 ms, 35 ms, 40 ms, 45 ms, 50 ms, 55 ms, 60 ms, 65ms, 70 ms, 75 ms, 80 ms, 85 ms, 90 ms, 95 ms, 100 ms, 200 ms, 300 ms,400 ms, 500 ms, 600 ms, 700 ms, 800 ms, 900 ms, 1 s, 2 s, 3 s, 4 s, 5 s,6 s, 7 s, 8 s, 9 s or 10 s.

The first ion guide is preferably arranged and adapted to receive a beamof ions from the ion mobility spectrometer or separator and to convertor partition the beam of ions such that at least 1, 2, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 separate groups orpackets of ions are confined and/or isolated in the first ion guide atany particular time, and wherein each group or packet of ions isseparately confined and/or isolated in a separate axial potential wellformed in the first ion guide. The average ion mobility of ions in eachof the groups or packets of ions confined and/or isolated in the firstion guide preferably progressively decreases with time and/orprogressively decreases from the exit region of the first ion guidetowards the entrance region of the first ion guide.

The first voltage means is preferably arranged and adapted to create atleast 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19or 20 separate axial potential wells which are preferably substantiallysimultaneously translated along at least 5%, 10%, 15%, 20%, 25%, 30%,35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100%of the length of the first ion guide.

A second voltage means is preferably arranged and adapted to create atleast 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19or 20 separate axial potential wells which are preferably substantiallysimultaneously translated along at least 5%, 10%, 15%, 20%, 25%, 30%,35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100%of the length of the second ion guide.

The first ion guide is preferably arranged and adapted to retain and/orconfine and/or partition ions emerging from the ion mobilityspectrometer or separator and to translate ions in one or more groups orpackets of ions along at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%,45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of theaxial length of the first ion guide whilst either: (i) substantiallymaintaining the order and/or fidelity in which ions emerge from the ionmobility spectrometer or separator; and/or (ii) substantiallymaintaining the composition of ions as one or more groups or packets ofions are translated along the first ion guide.

According to the preferred embodiment the mass spectrometer preferablyfurther comprises an ion trap upstream of the ion mobility spectrometeror separator. The ion trap is preferably arranged and adapted torepeatedly pulse ions into the ion mobility spectrometer or separator.

According to the preferred embodiment the second ion guide preferablyhas a cycle time which either: (i) substantially corresponds with acycle time of the ion mobility spectrometer or separator; or (ii)substantially differs from a cycle time of the ion mobility spectrometeror separator.

In a mode of operation the second ion guide is preferably arranged andadapted to trap, store or accumulate ions in an ion trapping regionlocated towards, near or substantially at the exit of the second ionguide. Ions are preferably periodically released from the ion trappingregion of the second ion guide and are preferably passed to the ionmobility spectrometer or separator.

The mass spectrometer preferably comprises means arranged and adapted tomaintain at least a portion of the second ion guide at a pressureselected from the group consisting of: (i) >0.0001 mbar; (ii) >0.001mbar; (iii) >0.01 mbar; (iv) >0.1 mbar; (v) >1 mbar; (vi) >10 mbar;(vii) 0.0001-0.1 mbar; and (viii) 0.001-0.01 mbar.

The mass spectrometer preferably comprises acceleration means arrangedand adapted to accelerate ions into the second ion guide so that atleast some ions are caused to fragment upon entering the second ionguide. The mass spectrometer preferably further comprises means arrangedand adapted to optimise the energy of ions prior to entering the secondion guide so that the ions are preferably caused to fragment in asubstantially optimal manner.

According to the preferred embodiment there is provided a control systemarranged and adapted to switch or repeatedly switch the potentialdifference through which ions pass prior to entering the second ionguide between a first mode of operation wherein ions are substantiallyfragmented upon entering the second ion guide and a second mode ofoperation wherein substantially less ions are fragmented or whereinsubstantially no ions are fragmented upon entering the second ion guide.

In the first mode of operation ions entering the second ion guide arepreferably accelerated through a potential difference selected from thegroup consisting of: (i) ≥10 V; (ii) ≥20 V; (iii) ≥30 V; (iv) ≥40 V; (v)≥50 V; (vi) ≥60 V; (vii) ≥70 V; (viii) ≥80 V; (ix) ≥90 V; (x) ≥100 V;(xi) ≥110 V; (xii) ≥120 V; (xiii) ≥130 V; (xiv) ≥140 V; (xv) ≥150 V;(xvi) ≥160 V; (xvii) ≥170 V; (xviii) ≥180 V; (xix) ≥190 V; and (xx) ≥200V.

In the second mode of operation ions entering the second ion guide arepreferably accelerated through a potential difference selected from thegroup consisting of: (i) ≤20 V; (ii) ≤15 V; (iii) ≤10 V; (iv) ≤5V; and(v) ≤1V.

The control system is preferably arranged and adapted to switch thesecond ion guide between the first mode of operation and the second modeof operation at least once every 1 ms, 5 ms, 10 ms, 15 ms, 20 ms, 25 ms,30 ms, 35 ms, 40 ms, 45 ms, 50 ms, 55 ms, 60 ms, 65 ms, 70 ms, 75 ms, 80ms, 85 ms, 90 ms, 95 ms, 100 ms, 200 ms, 300 ms, 400 ms, 500 ms, 600 ms,700 ms, 800 ms, 900 ms, 1 s, 2 s, 3 s, 4 s, 5 s, 6 s, 7 s, 8 s, 9 s or10 s.

According to an embodiment the mass spectrometer preferably furthercomprises a fragmentation or collision cell for fragmenting ions byCollision Induced Dissociation (“CID”) upon colliding with or impactinggas or other molecules.

According to an alternative embodiment the mass spectrometer preferablyfurther comprises a fragmentation device for fragmenting ions, thefragmentation device selected from the group consisting of: (i) aSurface Induced Dissociation (“SID”) fragmentation device; (ii) anElectron Transfer Dissociation fragmentation device; (iii) an ElectronCapture Dissociation 11 fragmentation device; (iv) an Electron Collisionor Impact Dissociation fragmentation device; (v) a Photo InducedDissociation (“PID”) fragmentation device; (vi) a Laser inducedDissociation fragmentation device; (vii) an infrared radiation induceddissociation device; (viii) an ultraviolet radiation induceddissociation device; (ix) an ion-molecule reaction fragmentation device;(x) a nozzle-skimmer interface fragmentation device; (xi) an in-sourcefragmentation device; (xii) an ion-source Collision Induced Dissociationfragmentation device; (xiii) a thermal or temperature sourcefragmentation device; (xiv) an electric field induced fragmentationdevice; (xv) a magnetic field induced fragmentation device; and (xvi) anenzyme digestion or enzyme degradation fragmentation device.

According to a preferred embodiment the mass spectrometer preferablyfurther comprises a mass filter, a quadrupole rod set mass filter, aTime of Flight mass analyser, a Wein filter or a magnetic sector massanalyser arranged upstream and/or downstream of the second ion guide.

A further ion guide may be provided upstream and/or downstream of thesecond ion guide and is preferably arranged upstream of a mass filterand downstream of an ion source.

The further ion guide preferably comprises: (i) a multipole rod set or asegmented multipole rod set; (ii) an ion tunnel or ion funnel; or (iii)a stack or array of planar, plate or mesh electrodes.

The multipole rod set preferably comprises a quadrupole rod set, ahexapole rod set, an octapole rod set or a rod set comprising more thaneight rods.

The ion tunnel or ion tunnel preferably comprises a plurality ofelectrodes or at least 2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90 or 100electrodes having apertures through which ions are transmitted in use,wherein at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%,60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the electrodes haveapertures which are of substantially the same size or area or which haveapertures which become progressively larger and/or smaller in size or inarea. Preferably, at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%,50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of theelectrodes have internal diameters or dimensions selected from the groupconsisting of: (i) ≤1.0 mm; (ii) ≤2.0 mm; (iii) ≤3.0 mm; (iv) ≤4.0 mm;(v) ≤5.0 mm; (vi) ≤6.0 mm; (vii) ≤7.0 mm; (viii) ≤8.0 mm; (ix) ≤9.0 mm;(x) ≤10.0 mm; and (xi) >10.0 mm.

The stack or array of planar, plate or mesh electrodes preferablycomprises a plurality or at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19 or 20 planar, plate or mesh electrodesarranged generally in the plane in which ions travel in use, wherein atleast 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%,70%, 75%, 80%, 85%, 90%, 95% or 100% of the planar, plate or meshelectrodes are arranged generally in the plane in which ions travel inuse. The mass spectrometer preferably further comprises AC or RF voltagemeans for supplying the plurality of planar, plate or mesh electrodeswith an AC or RF voltage and wherein adjacent plate or mesh electrodesare supplied with opposite phases of the AC or RF voltage.

The further ion guide preferably further comprises a plurality of axialsegments or at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65,70, 75, 80, 85, 90, 95 or 100 axial segments.

Transient DC voltage means may be arranged and adapted to apply one ormore transient DC voltages or potentials or one or more transient DCvoltage or potential waveforms to electrodes forming the further ionguide in order to urge at least some ions along at least 5%, 10%, 15%,20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%,90%, 95% or 100% of the axial length of the further ion guide.Alternatively, AC or RF voltage means may be provided which arepreferably arranged and adapted to apply two or more phase-shifted AC orRF voltages to electrodes forming the further ion guide in order to urgeat least some ions along at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%,45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of theaxial length of the further ion guide.

The mass spectrometer preferably further comprises a transfer device, anEinzel lens or ion optical lens arrangement arranged between the firstion guide and the mass analyser.

The mass spectrometer preferably further comprises an ion source. Theion source may be selected from the group consisting of: (i) anElectrospray ionisation (“ESI”) ion source; (ii) an Atmospheric PressurePhoto Ionisation (“APPI”) ion source; (iii) an Atmospheric PressureChemical Ionisation (“APCI”) ion source; (iv) a Matrix Assisted LaserDesorption Ionisation (“MALDI”) ion source; (v) a Laser DesorptionIonisation (“LDI”) ion source; (vi) an Atmospheric Pressure Ionisation(“API”) ion source; (vii) a Desorption Ionisation On Silicon (“DIOS”)ion source; (viii) an Electron Impact (“EI”) ion source; (ix) a ChemicalIonisation (“CI”) ion source; (x) a Field Ionisation (“FI”) ion source;(xi) a Field Desorption (“FD”) ion source; (xii) an Inductively CoupledPlasma (“ICP”) ion source; (xiii) a Fast Atom Bombardment (“FAB”) ionsource; (xiv) a Liquid Secondary Ion Mass Spectrometry (“LSIMS”) ionsource; (xv) a Desorption Electrospray Ionisation (“DESI”) ion source;(xvi) a Nickel-63 radioactive ion source; and (xvii) an AtmosphericPressure Matrix Assisted Laser Desorption Ionisation ion source. The ionsource may comprise a pulsed or continuous ion source.

The mass analyser preferably comprises a Time of Flight mass analyser oran axial or orthogonal acceleration Time of Flight mass analyser. Themass analyser preferably comprises a pusher and/or puller electrodewherein ions are released from the first ion guide into the Time ofFlight mass analyser at a first time and arrive in a region in thevicinity of the pusher and/or puller electrode. The pusher and/or pullerelectrode is then preferably energized after a delay time subsequent tothe first time. The mass analyser is preferably arranged and adaptedsuch that the delay time is preferably progressively varied orincreased. The delay time may be set such “that ions having a desiredcharge state are substantially orthogonally accelerated whereas ionshaving an undesired charge state are not substantially orthogonallyaccelerated. The desired charge state and/or the undesired charge statemay be selected from the group consisting of: (i) ions having a singlecharge; (ii) ions having two charges; (iii) ions having three charges;(iv) ions having four charges; (v) ions having five charges; (vi) ionshaving more than five charges; and (vii) multiply charged ions.

A first plurality of ions are preferably pulsed into the ion mobilityspectrometer or separator and prior to a second plurality of ions beingpulsed into the ion mobility spectrometer or separator the pusher and/orpuller electrode is preferably energised at least x times, wherein x isselected from the group consisting of: (i) 1; (ii) 2-10; (iii) 10-20;(iv) 20-30; (v) 30-40; (vi) 40-50; (viii) 50-60; (ix) 60-70; (x) 70-80;(xi) 80-90; (xii) 90-100; (xiii) 100-110; (xiv) 110-120; (xv) 120-130;(xvi) 130-140; (xvii) 140-150; (xviii) 150-160; (xix) 160-170; (xx)170-180; (xxi) 180-190; (xxii) 190-200; (xxiii) 200-210; (xxiv) 210-220;(xxv) 220-230; (xxvi) 230-240; (xxvii) 240-250; and (xxviii) >250.

The pusher and/or puller electrode is preferably energized once every0-10 μs, 10-20 μs, 20-30 μs, 30-40 μs, 40-50 [mu]s, 50-60 μs, 60-70 μs,70-80 μs, 80-90 μs, 90-100 μs, 100-110 μs, 110-120 μs, 120-130 μs,130-140 μs, 140-150 μs, 150-160 μs, 160-170 μs, 170-180 μs, 180-190 μs,190-200 μs, 200-210 μs, 210-220 μs, 220-230 μs, 230-240 μs, 240-250 μs,250-260 μs, 260-270 μs, 270-280 μs, 280-290 μs 290-300 μs or >300 μs.

The pusher and/or puller electrode is preferably energized at least 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20or >20 times for every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20 or >20 axial potential wells which are translatedto the end of the first ion guide such that ions are caused to beemitted or otherwise ejected from the first ion guide.

According to the preferred embodiment a first plurality of ions arepulsed into the ion mobility spectrometer or separator and prior to asecond plurality of ions being pulsed into the ion mobility spectrometeror separator at least y separate axial potential wells are created orformed in the first ion guide and/or are translated along at least aportion of the axial length of the first ion guide, wherein y isselected from the group consisting off: (i) 1; (ii) 2-10; (iii) 10-20;(iv) 20-30; (v) 30-40; (vi) 40-50; (viii) 50-60; (ix) 60-70; (x) 70-80;(xi) 80-90; (xii) 90-100; (xiii) 100-110; (xiv) 110-120; (xv) 120-130;(xvi) 130-140; (xvii) 140-150; (xviii) 150-160; (xix) 160-170; (XX)170-180; (xxi) 180-190; (xxii) 190-200; (xxiii) 200-210; (xxiv) 210-220;(xxv) 220-230; (xxvi) 230-240; (xxvii) 240-250; and (xxviii) >250.

According to less preferred embodiment the mass analyser may be selectedfrom the group consisting of: (i) a quadrupole mass analyser; (ii) a 2Dor linear quadrupole mass analyser; (iii) a Paul or 3D quadrupole massanalyser; (iv) a Penning trap mass analyser; (v) an ion trap massanalyser; (vi) a magnetic sector mass analyser; (vii) Ion CyclotronResonance (“ICR”) mass analyser; (viii) a Fourier Transform IonCyclotron Resonance (“FTICR”) mass analyser; (ix) an electrostatic ororbitrap mass analyser; (x) a FouJtrier Transform electrostatic ororbitrap mass analyser; and (xi) a Fourier Transform mass analyser.

According to an embodiment the mass spectrometer preferably furthercomprises processing means wherein the processing means is arranged andadapted to filter mass spectral data obtained by the mass analyser sothat a mass spectrum is produced comprising mass spectral data relatingto: (i) ions having a single charge; (ii) ions having two charges; (iii)ions having three charges; (iv) ions having four charges; (v) ionshaving five charges; (vi) ions having more than five charges; and (vii)multiply charged ions.

According to another aspect of the present invention there is provided amethod of mass spectrometry comprising:

separating ions in an ion mobility spectrometer or separator;

receiving ions from the ion mobility separator or spectrometer into afirst ion guide arranged downstream of the ion mobility spectrometer orseparator, the first ion guide comprising a plurality of electrodes;

applying one or more voltages or one or more voltage waveforms to theelectrodes of the first ion guide so that in a first mode of operationions received from the ion mobility spectrometer or separator aretrapped and/or transported and/or translated in separate regions orportions of the first ion guide; and

providing a mass analyser downstream of the first ion guide.

According to another aspect of the present invention there is provided amass spectrometer comprising an ion guide arranged downstream of an ionmobility spectrometer or separator, wherein in use one or more transientDC voltages or potentials or one or more transient DC voltage orpotential waveforms are applied to the ion guide in order to create aplurality of axial potential wells in the ion guide.

According to another aspect of the present invention there is provided amass spectrometer comprising an ion guide arranged downstream of an ionmobility spectrometer or separator, wherein in use two or morephase-shifted AC or RF voltages are applied to the ion guide in order tocreate a plurality of axial potential wells in the ion guide.

According to another aspect of the present invention there is provided amass spectrometer comprising an ion guide arranged downstream of an ionmobility spectrometer or separator, wherein in use a plurality of axialpotential wells are created in the ion guide and/or are translated alongthe ion guide.

According to another aspect of the present invention there is provided amethod of mass spectrometry comprising:

providing an ion guide downstream of an ion mobility spectrometer orseparator; and

applying one or more transient DC voltages or potentials or one or moretransient DC voltage or potential waveforms to the ion guide in order tocreate a plurality of axial potential wells in the ion guide.

According to another aspect of the present invention there is provided amethod of mass spectrometry comprising:

providing an ion guide arranged downstream of an ion mobilityspectrometer or separator; and

applying two or more phase-shifted AC or RF voltages to the ion guide inorder to create a plurality of axial potential wells in the ion guide.

According to another aspect of the present invention there is provided amethod of mass spectrometry comprising:

providing an ion guide arranged downstream of an ion mobilityspectrometer or separator; and

creating a plurality of axial potential wells in the ion guide and/ortranslating a plurality of axial potential wells along the ion guide.

The preferred embodiment relates to a mass spectrometer and a method ofmass spectrometry wherein ions having certain specific charge states(e.g. multiply charged ions) can be separated from ions having othercharge states (e.g. singly charged ions) using an ion mobilityspectrometer or separator. The ions are then preferably passed to an ionguide in which a plurality of axial potential wells are created andwhich are then preferably translated along the length of the ion guide.

The ion guide is preferably arranged and adapted to preserve thefidelity and composition of groups or packets of ions as they emergefrom the ion mobility spectrometer or separator and as are received bythe ion guide. The ion guide also preferably enables the sampling dutycycle of a Time of Flight mass analyser arranged downstream of the ionguide to be optimised.

A method of mass spectrometry according to a preferred embodiment of thepresent invention comprises: providing a pulse of ions and performingthe following steps before providing another pulse of ions: (a)temporally separating at least some of the ions according to their ionmobility in an ion mobility spectrometer or separator; (b) collecting atleast some of the ions which emerge from the ion mobility spectrometeror separator in an ion guide and partitioning the ions received in theion guide into groups or packets with a series of potential hills orbarriers separating each group of ions and wherein the ions arepartitioned according to their arrival times at the exit of the ionmobility spectrometer or separator; (c) transporting the ions in the ionguide wherein the ions are confined radially by an inhomogeneous RFelectric field and are propelled or urged forwards along the ion guideby the series of potential hills or barriers which move or are otherwisetranslated along the axis of the ion guide; and (d) recording the massspectrum of ions in one or more groups or packets of ions which arepropelled or urged forwards to the exit of the ion guide by one or moreof the series of potential hills or barriers.

The mass spectrometer is preferably capable of recording the full orpartial mass spectrum of a packet of ions. The mass spectrometer may,for example, comprise a Time of Flight mass analyser. An orthogonalacceleration Time of Flight mass analyser is particularly preferred.According to other embodiments the mass analyser may comprise a linearquadrupole ion trap mass analyser, a 3D quadrupole ion trap massanalyser, an orbitrap mass analyser, a Penning trap mass analyser or anion cyclotron trap mass analyser. The mass analyser may comprise avariant of the aforementioned mass analysers employing FourierTransforms of mass dependent resonance frequencies.

By recording the full or partial mass spectrum of the ions in eachpacket of ions transmitted by the ion guide any desired charge statepresent in a complex mixture of ions may be detected and thenpreferentially selected or displayed when generating a final massspectrum. Mass spectral data relating to ions having undesired chargestates may either not be recorded or may be removed or otherwisefiltered so that such mass spectral data is not displayed in the finalmass spectrum.

In a preferred embodiment the mass spectrometer comprises an orthogonalacceleration Time of Flight mass analyser. In a conventional Time ofFlight mass spectrometer ions are arranged to possess approximately thesame energy and are then passed to an orthogonal acceleration regionadjacent a pusher electrode. An orthogonal acceleration electric fieldis periodically applied to the orthogonal acceleration region byenergising the pusher electrode. The length of the orthogonalacceleration region, the energy of the ions and the frequency of theapplication of the orthogonal acceleration electric field will determinethe sampling duty cycle of the ions. Ions having approximately the sameenergy but having different mass to charge ratios will have differentvelocities and hence will have different sampling duty cycles.

In contrast to conventional arrangements, according to the preferredembodiment ions are preferably released from an ion guide upstream of anorthogonal acceleration Time of Flight mass analyser. The ions arepreferably released in a succession of packets from the ion guidewherein preferably all the ions in a packet of ions released from theion guide will preferably have a relatively narrow range of mass tocharge ratios and therefore velocities. As a result, substantially allthe ions in a packet of ions released from the ion guide can be arrangedso as to arrive at the orthogonal acceleration region of the Time ofFlight mass analyser at a time when an orthogonal acceleration electricfield is applied. As a result, a relatively high sampling duty cycle canbe achieved for most or preferably all of the ions being ejected orreleased from the ion guide.

In order to achieve a relatively high sampling duty cycle it isdesirable that each packet of ions is released from the ion guide suchthat the time for the ions contained in a packet of ions to arrive atthe orthogonal acceleration region is sufficiently short such that theions do not disperse in the axial direction to a greater extent than thewidth of the orthogonal acceleration region (which substantiallycorresponds with the width of the pusher electrode). Accordingly, thedistance from the point of release of the ions from the ion guide to theorthogonal acceleration region of the Time of Flight mass analyser ispreferably sufficiently short given the energy of the ions and the rangeof mass to charge ratios of the ions contained within each packet ofions. The range of mass to charge ratios of ions within each packet ofions translated along the ion guide is preferably arranged to berelatively narrow or small. The orthogonal acceleration electric fieldis preferably applied in synchronism with the arrival of the ions at theorthogonal acceleration region. According to the preferred embodiment itis possible to achieve a sampling duty cycle of substantially 100% forall the ions in a packet of ions released from the ion guide.Furthermore, if the optimum conditions apply for each and every packetof ions released from the ion guide, then an overall sampling duty cycleapproaching 100% may be achieved according to the preferred embodiment.

The preferred embodiment preferably comprises an ion mobilityspectrometer or separator which is preferably coupled to a massanalyser, preferably an orthogonal acceleration Time of Flight massanalyser via an intermediate ion guide. The preferred embodimentpreferably enables ions to be separated according to their charge stateand preferably enables a relatively high sampling duty cycle to beobtained for ions having a wide range of mass to charge ratios.

A particularly preferred aspect of the present invention is that an ionguide is preferably positioned or otherwise located between an ionmobility spectrometer or separator and a mass analyser. Ions arepreferably transported in and along the ion guide by a succession ofpotential hills or barriers which are preferably created within the ionguide. As a result, a plurality of axial potential wells are preferablycreated in the ion guide which preferably move or are otherwisetranslated along the axis of the ion guide. The ion mobilityspectrometer or separator and the ion guide are preferably sufficientlyclosely coupled such that ions emerging from the exit of the ionmobility spectrometer or separator are preferably received in successiveaxial potential wells created in the ion guide. According to thepreferred embodiment the order or composition of the ions emerging fromthe exit of the ion mobility spectrometer or separator is preferablymaintained or otherwise preserved as the ions become trapped indifferent or separate axial potential wells in the ion guide. Anorthogonal acceleration Time of Flight mass analyser is preferablypositioned downstream of the ion guide in order to mass analyse ions asthey emerge or are released from the ion guide. The ion guide and theorthogonal acceleration Time of Flight mass analyser are also preferablysufficiently closely coupled such that each packet or group of ionsreleased from the exit of the ion guide is then preferably sampled bythe orthogonal acceleration Time of Flight mass analyser with a samplingduty cycle which may approach substantially 100% according to thepreferred embodiment.

Ions passing through the preferred ion mobility spectrometer orseparator are preferably subjected to an electric field in the presenceof a buffer gas. Different species of ion will preferably acquiredifferent velocities and will preferably become separated according totheir ion mobility as they pass through the preferred ion mobilityspectrometer or separator. The mobility of an ion in the ion mobilityspectrometer or separator will preferably depend upon the size, shapeand charge state of the ion. One form of ion mobility spectrometer orseparator which may be used comprises a drift tube or cell wherein anaxial electric field is applied along the length of the drift tube orcell and a relatively high pressure buffer gas is provided. Ions havingrelatively high ion mobilities will preferably pass faster through theion mobility spectrometer or separator than ions having relatively lowerion mobilities. Ions are therefore preferably separated according totheir ion mobility in the ion mobility spectrometer or separator. In oneembodiment the drift tube or cell may also act as an ion guide in thations are radially confined within the drift tube or cell by theapplication of an inhomogeneous RF field to electrodes forming the ionmobility spectrometer or separator. However, according to otherembodiments ions may not be radially confined within the drift tube orcell.

According to a preferred embodiment the ion mobility spectrometer orseparator preferably comprises a plurality of electrodes wherein ionsare radially confined within the ion mobility spectrometer or separatorby the application of an inhomogeneous RF electric field to theelectrodes. The electrodes preferably comprise a plurality of electrodeshaving apertures through which ions are transmitted in use. Ions may beurged forwards through the ion mobility spectrometer or separator by oneor more potential hills or one or more transient DC voltages orpotentials which are preferably arranged to move along the axis of thepreferred ion mobility spectrometer or separator in the presence of abuffer gas. Appropriate selection of the amplitude and velocity of theone or more potential hills or the one or more transient DC voltages orpotentials and the type and pressure of the buffer gas can ensure thatat least some ions are able to selectively slip or otherwise pass overthe one or more potential hills or one or more transient DC voltages orpotentials as they are translated forward. Ions will thereforepreferably be differentially affected by the translation of the one ormore potential hills in a manner dependent upon their ion mobility. As aresult ions having different ion mobilities are preferably transportedat different velocities through the ion mobility spectrometer orseparator and become separated depending upon or according to their ionmobility.

The cycle time for separating a group of ions according to their ionmobility in the preferred ion mobility spectrometer or separator may bebetween 2 and 50 ms, preferably between 5 and 20 ms and furtherpreferably about 10 ms. The cycle time for mass analysing a packet ofions using a Time of Flight mass analyser may be between 10 and 250 μs,preferably between 20 and 125 μs, and further preferably about 50 μs.

As an illustrative example only, ions may be separated according totheir ion mobility in a preferred ion mobility spectrometer or separatorover a time period of approximately 10 ms. The ions emerging from thepreferred ion mobility spectrometer or separator may then be collectedin one of 200 separate axial potential wells which are preferablysuccessively created in the ion guide which are then preferablysubsequently translated along the length of the ion guide. Ions emergingfrom an axial potential well as the axial potential well reaches theexit of the preferred ion guide may then be mass analysed in a timeperiod of 50 μs. For each cycle of creating an axial potential well andtranslating the axial potential well along the length of the ion guidethere is preferably also a corresponding cycle or orthogonalacceleration and mass analysis of ions by the Time of Flight massanalyser. According to the preferred embodiment the delay time betweenthe release of a packet of ions from the ion guide and the subsequentapplication of an orthogonal acceleration voltage to a pusher electrodedisposed adjacent the orthogonal acceleration region of the Time ofFlight mass analyser is preferably progressively increased. The delaytime is preferably increased since the average mass to charge ratio ofions released from successive potential wells as they reach the exit ofthe ion guide also preferably increases reflecting the fact that forions having a particular charge state lower mass to charge ratio ionswill emerge from the exit of the ion mobility spectrometer or separatorprior to relatively higher mass to charge ratio ions.

An ion source is preferably arranged upstream of the preferred ionmobility spectrometer or separator and may comprise a pulsed ion sourcesuch as a Laser Desorption Ionisation (“LDI”) ion source, a MatrixAssisted Laser Desorption Ionisation (“MALDI”) ion source or aDesorption Ionisation on Silicon (“DIOS”) ion source. Alternatively, acontinuous ion source may be used in which case an ion trap upstream ofthe preferred ion mobility spectrometer or separator may be provided.The ion trap is preferably arranged to store ions received from the ionsource and periodically to release the ions into or towards the ionmobility spectrometer or separator. The continuous ion source maycomprise an Electrospray Ionisation (“ESI”) ion source, an AtmosphericPressure Chemical Ionisation (“APCI”) ion source, an Electron Impact(“EI”) ion source, an Atmospheric Pressure Photon Ionisation (“APPI”)ion source, a Chemical Ionisation (“CI”) ion source, a Fast AtomBombardment (“FAB”) ion source, a Liquid Secondary Ion Mass Spectrometry(“LSIMS”) ion source, a Field Ionisation (“FI”) ion source or a FieldDesorption (“FD”) ion source. Other pulsed, continuous orpseudo-continuous ion sources may also be used. An Atmospheric PressureIonisation ion source is particularly preferred.

The mass spectrometer may further comprise a mass filter or massanalyser preferably arranged downstream of the ion source and preferablyarranged upstream of the preferred ion mobility spectrometer orseparator. The mass filter or mass analyser may, for example, be used totransmit specific parent or precursor ions having a specific mass tocharge ratio or having mass to charge ratios within a particular rangeto the preferred ion mobility spectrometer or separator. The mass filtermay, for example, comprise a quadrupole rod set mass filter, a Time ofFlight mass analyser, a Wein filter or a magnetic sector mass analyser.

The mass spectrometer may comprise a collision or fragmentation cellpreferably arranged upstream of the preferred ion mobility spectrometeror separator. In one mode of operation at least some parent or precursorions entering the collision or fragmentation cell may be caused tofragment. The resulting daughter, fragment or product ions are thenpreferably transmitted to the preferred ion mobility spectrometer orseparator. The daughter, fragment or product ions are then preferablyseparated in the preferred ion mobility spectrometer or separatoraccording to their ion mobility.

Although an orthogonal acceleration Time of Flight mass analyser isparticularly preferred, according to other less preferred embodimentsthe mass spectrometer may comprise a quadrupole mass analyser, a 3D iontrap mass analyser, a linear ion trap mass analyser, a Fourier TransformIon Cyclotron Resonance mass analyser, a Fourier Transform Orbitrap massanalyser or a magnetic sector mass analyser.

BRIEF DESCRIPTION OF THE DRAWINGS

Various embodiments of the present invention together with otherarrangements given for illustrative purposes only will now be described,by way of example only, and with reference to the accompanying drawingsin which:

FIG. 1 shows a portion of a mass spectrum obtained conventionallywherein doubly charged analyte ions of interest are partially obscuredamongst a background of singly charged ions;

FIG. 2A shows a portion of a mass spectrum obtained conventionally usingnormal detector gain and FIG. 2B shows a comparable mass spectrumobtained by lowering the detector gain;

FIG. 3A illustrates the known relationship between the drift time ofions through an ion mobility spectrometer or separator and thesubsequent time of flight of the ions (which is directly related to themass to charge ratio of the ion) in a Time of Flight mass analyser driftregion for various singly and doubly charged ions and FIG. 3B shows anexperimentally determined relationship between the drift time of amixture of singly and doubly charged ions through an ion mobilityspectrometer or separator and their mass to charge ratio;

FIG. 4A shows a conventional mass spectrometer comprising an ionmobility spectrometer or separator coupled to a Time of Flight massanalyser via a transfer lens and FIG. 4B illustrates how a first packetof ions may be gated into an ion mobility spectrometer or separator andthe ions emerging from the ion mobility spectrometer or separator arethen repeatedly pulsed into the drift region of an orthogonalacceleration Time of Flight mass analyser before a second packet of ionsis gated into the ion mobility spectrometer or separator;

FIG. 5 illustrates the general principle of how ions having a certaincharge state may be recognised or selected from mass spectral dataobtained by coupling an ion mobility spectrometer or separator to a Timeof Flight mass analyser;

FIG. 6 shows a first preferred embodiment of the present inventionwherein an ion guide in which a plurality of axial potential wells arecreated is used to interface an ion mobility spectrometer or separatorto an orthogonal acceleration Time of Flight mass analyser;

FIG. 7A shows an embodiment of the present invention wherein an ion trapis arranged upstream of an ion mobility spectrometer or separator inorder to pulse ions into the ion mobility spectrometer or separator andan ion guide in which a plurality of axial potential wells are createdis provided downstream at the ion mobility spectrometer or separator andupstream of a Time of Flight mass analyser, FIG. 7B shows the potentialprofile for an ion trap, ion mobility spectrometer or separator and anion guide according to an embodiment of the present invention wherein atrapping DC voltage is applied to the ion trap, a constant DC voltagegradient is maintained across the ion mobility spectrometer or separatorand a plurality of axial potential wells are formed in the ion guidewhich are then translated towards the exit of the ion guide and FIG. 7Cshows the potential profile for an ion trap, ion mobility spectrometeror separator and an ion guide according to an embodiment of the presentinvention wherein a plurality of relatively low amplitude transient DCpotentials are applied to the electrodes of the ion mobilityspectrometer or separator in order to separate ions according to theirion mobility;

FIG. 8 illustrates a conventional arrangement wherein ions having arelatively wide range of mass to charge ratios are non-mass selectivelyreleased from an ion trap upstream of an orthogonal acceleration Time ofFlight mass analyser and will have a spatial spread which exceeds thewidth of the orthogonal acceleration region of a Time of Flight massanalyser by the time that the ions reach the orthogonal accelerationregion;

FIG. 9 illustrates the relatively low sampling duty cycle obtained whenions are continuously passed into a Time of Flight mass analyser andions are periodically sampled and also how pulsing ions into a Time ofFlight mass analyser and setting an appropriate delay time of theorthogonal acceleration pulse enables the sampling duty cycle to beincreased only for some ions;

FIG. 10 shows how ions which are released from an axial potential wellat the exit of an ion guide according to the preferred embodiment of thepresent invention do not become significantly spatially separated by thetime that the ions reach the orthogonal acceleration region of anorthogonal acceleration Time of Flight mass analyser since the ions ineach packet of ions released from the ion guide will have substantiallysimilar mass to charge ratios;

FIG. 11 shows some experimental results and demonstrates how thesampling duty cycle can be significantly improved to >80% for ionshaving a wide range of mass to charge ratios according to an embodimentof the present invention whereas the typical average conventionalsampling duty cycle is only approximately 15%;

FIG. 12 shows a second preferred embodiment of the present inventionwherein a second ion guide is provided upstream of the ion mobilityspectrometer or separator and wherein a plurality of axial potentialwells are preferably created within and translated along the length ofthe second ion guide;

FIG. 13A shows a mass spectrum obtained conventionally and FIG. 13Bshows a comparable mass spectrum obtained by enhancing the sampling dutycycle in a manner according to an embodiment of the present invention;

FIG. 14A shows in greater detail a portion of the mass spectrum obtainedconventionally and which is shown in FIG. 13A, FIG. 14B shows in greaterdetail a corresponding portion of the mass spectrum obtained byenhancing the sampling duty cycle in a manner according to an embodimentof the present invention and FIG. 14C shows a corresponding portion of amass spectrum obtained according to a particularly preferred embodimentof the present invention wherein the sampling duty cycle was enhanced ina manner according to an embodiment of the present invention and whereinthe mass spectral data was also post-processed so that only ions havinga particular charge state were displayed in the final mass spectrum; and

FIG. 15A shows in greater detail a different portion of the massspectrum obtained conventionally and which is shown in FIG. 13A, FIG.15B shows in greater detail a corresponding portion of the mass spectrumobtained by enhancing the sampling duty cycle in a manner according toan embodiment of the present invention and FIG. 15C shows acorresponding portion of a mass spectrum obtained according to aparticularly p referred embodiment of the present invention wherein thesampling duty cycle was enhanced in a manner according to an embodimentof the present invention and wherein the mass spectral data was alsopost-processed so that only ions having a particularly charge state weredisplayed in the final mass spectrum.

DETAIL DESCRIPTION OF THE PREFERRED EMBODIMENTS

FIG. 1 shows a typical mass spectrum obtained conventionally andillustrates how doubly charged analyte ions of potential interest may berelatively obscured amongst a background of singly charged ions. Beingable effectively to filter out singly charged ions which relate tochemical noise so that the mass spectrometer can more easily targetmultiply charged peptide related ions would be particularly advantageousfor the study of protein digests. Where chemical noise is not thelimitation to detection then it would still nonetheless be advantageousto be able to increase the transmission and sampling efficiency ofanalyte ions of interest thereby improving the sensitivity of the massspectrometer. As will be discussed, the preferred embodiment of thepresent invention advantageously enables chemical noise (e.g. singlycharged ions) to be reduced or substantially removed from the final massspectrum and the preferred embodiment also preferably enables thetransmission and sampling duty cycle of analyte ions of interest to beincreased. The preferred embodiment is therefore particularlyadvantageous in the study of protein digests.

For illustrative purposes only some conventional approaches to reducingthe effect of singly charged background ions which may obscure multiplycharged analyte ions of interest will now be discussed. It is know tooperate an ion detector so as to favour the detection of multiplycharged ions relative to singly charged ions. The ion detector of anorthogonal acceleration Time of Flight mass analyser may, for example,count the arrival of ions using a Time to Digital Converter (“TDC”)which may have a certain discriminator threshold. The voltage pulseproduced by a single ion arriving at the ion detector must be highenough to exceed the voltage threshold thereby triggering thediscriminator and so registering the arrival of an ion. The ion detectorproducing the voltage pulse may comprise an electron multiplier or aMicrochannel plate (“MCP”) detector. These detectors are chargesensitive so that the size of the signal they produce increases withincreasing charge state of the ions detected. Discrimination in favourof higher charge states can therefore be accomplished by increasing thediscriminator voltage level, lowering the detector gain, or by acombination of both approaches.

FIG. 2A shows a mass spectrum obtained conventionally with normaldetector gain. FIG. 2B shows a comparable mass spectrum obtained byreducing the detector gain. It can be seen from FIGS. 2A and 2B thatwhilst reducing the detector gain (or increasing the discriminatorlevel) discriminates in favour of multiply charged ions, a significantdisadvantage of this approach is that the sensitivity is adverselylowered. As can be seen from the ordinate axes of FIGS. 2A and 2B, thesensitivity is reduced by a factor of about ×4 when a lower detectorgain is employed. The approach of lowering the detector gain also doesnot make it possible to select ions having a particular charge state.Instead, the best that can be achieved is a reduction of the efficiencyof detection of lower charge states with respect to higher chargestates.

An alternative approach to being able to preferentially select ionshaving a particular charge state is made possible by coupling an ionmobility spectrometer or separator to a Time of Flight mass analyser.

Ions in an ion mobility spectrometer or separator are subjected to anelectric field in the presence of a buffer gas. Different species of ionwill acquire different velocities and will become temporally separatedaccording to their ion mobility as they pass through the ion mobilityspectrometer or separator. The mobility of an ion in such an ionmobility spectrometer or separator will depend upon the size, shape andcharge state of the ion. Relatively large ions with one charge willnormally have relatively lower mobilities than relatively small ionshaving a single charge. Also, ion having one charge will also normallyhave a lower ion mobility than an ion relating to the same compound butwhich has two charges.

One form of an ion mobility separator or spectrometer comprises a drifttube or cell along which an axial electric field is maintained. Arelatively high pressure buffer gas is maintained within the drift tubeor cell. The combination of an axial electric field and the relativelyhigh pressure background gas causes ions having a relatively high ionmobility to pass more quickly through the drift tube or cell compared toions having a relatively low ion mobility. Ions are therefore caused toseparate according to their ion mobility.

The ion mobility separator or spectrometer may operate at or aroundatmospheric pressure. Alternatively, the ion mobility separator orspectrometer may operate under a partial vacuum at a pressure down to aslow as about 0.01 mbar. The ion mobility spectrometer or separator maycomprise a plurality of electrodes having apertures through which ionsare transmitted in use. A DC voltage gradient may be maintained acrossat least a portion of the ion mobility spectrometer or separator and atleast some of the electrodes may be connected to an AC or RF voltagesupply. The frequency of the AC or RF voltage is typically in the range0.1-3.0 MHz. This form of ion mobility spectrometer or separator isparticularly advantageous in that the AC or RF voltage applied to theelectrodes causes a pseudo-potential well to be created which acts toconfine ions radially within the ion mobility spectrometer or separator.Radial confinement of the ions will result in higher ion transmissioncompared with an ion mobility separator or spectrometer which does notconfine ions radially.

In another form of ion mobility spectrometer or separator ions areconfined radially by an inhomogeneous RF field. Ions are urged forwardsthrough the ion mobility spectrometer or separator by a series ofrelatively low amplitude potential hills that move along the axis of theion mobility spectrometer or separator. A relatively high pressurebuffer gas is maintained within the ion mobility spectrometer orseparator. Appropriate selection of the amplitude and velocity of theplurality of potential hills together with appropriate selection of thetype and pressure of the buffer gas allows ions to selectively slip orpass over the relatively low amplitude potential hills in a manner whichis dependent upon the mobility of the ions. Accordingly, ions ofdifferent mobility will be transported at different velocities throughthe ion mobility spectrometer or separator and will therefore becometemporally separated according to their ion mobility.

By providing a Time of Flight mass analyser downstream of the ionmobility spectrometer or separator to receive ions emerging from the ionmobility spectrometer or separator it is possible to detect and recordonly those ions having certain desired charge states. Alternatively,mass spectral data relating to all ions may be obtained but the massspectral data may then be post-processed so as to filter out massspectral data relating to ions having undesired charge states. The finalmass spectrum can therefore be arranged to display only ions havingcertain desired charged states.

The combination of an ion mobility spectrometer or separator and a Timeof Flight mass analyser may advantageously be used, for example, togenerate a mass spectrum relating just to doubly charged ions from atryptic digest of a large protein. Ions of differing mobility will beseparated in the ion mobility spectrometer or separator and will havedifferent drift times. The orthogonal acceleration Time of Flight massanalyser then effectively provides a further separation of the ionsaccording to their mass to charge ratio. A resulting two dimensionalplot of flight time through the mass analyser against drift time throughthe ion mobility spectrometer or separator can be generated. An exampleof such a two dimensional plot is shown in FIG. 3A. It can be seen fromFIG. 3A that singly charged [M+H]⁺ ions lie on a certain characteristicline which is different to that of doubly charged [M+2H]²⁺ ions.Accordingly, the Time of Flight mass analyser can be used just to recordthe flight time just of ions having a desired mass to charge ratio.Alternatively, the Time of Flight mass analyser may be used to recordthe flight times of all ions having all mass to charge ratios and chargestates. The resulting mass spectral data may then be post-processed toselect and present a mass spectrum relating just to ions having certainspecific desired charge states.

A further experimentally determined relationship between the mass tocharge ratio of ions and their drift time through an ion mobilityspectrometer or separator is shown in FIG. 3B. As can be seen from FIGS.3A and 3B, a doubly charged ion having the same mass to charge ratio asa singly charged ion will take less time to drift through the ionmobility spectrometer or separator compared with a singly charged ion.Although the ordinate axis of FIG. 3A is given as the flight timethrough the flight region of a Time of Flight mass analyser, it will beappreciated that this correlates directly with the mass to charge ratioof the ion.

A known mass spectrometer is shown in FIG. 4A. According to thisarrangement ions 1 emitted from an Electrospray ion source are stored inan ion trap 2. The ions are then released periodically (at time T=0)from the ion trap 2 via a gate electrode 3. The ions then pass into thedrift cell of an ion mobility spectrometer or separator 4. As will beapparent from FIGS. 3A and 3B, the typical drift time of ions throughthe ion mobility spectrometer or separator 4 is of the order of a fewmilliseconds (ms).

After all the ions which were initially pulsed into the ion mobilityspectrometer or separator 4 have traversed the length of the ionmobility spectrometer or separator 4, a new pulse of ions is ejectedfrom the ion trap 2 and is admitted into the ion mobility spectrometeror separator 4. The process of separating ions in the ion mobilityspectrometer or separator 4 according to their ion mobility is thenrepeated.

The time taken for an ion to exit the ion mobility spectrometer orseparator 4 and arrive at the pusher electrode 10 of the Time of Flightmass analyser 13 which is arranged downstream of the ion mobilityspectrometer or separator 4 is a function of the ion mobility of theion. Ions having a relatively high ion mobility will take a relativelyshort time to transverse the ion mobility spectrometer or separator 4and reach the orthogonal acceleration region adjacent the pusherelectrode 10 of the Time of Flight mass analyser. Synchronisation of theenergisation of the pusher electrode 10 with that of the gate electrode3 at the entrance to the ion mobility spectrometer or separator 4enables the combination of the ion mobility spectrometer or separator 4and the Time of Flight mass analyser 13 to be used such that it ispossible to discriminate or select mass spectral data relating to ionshaving a particular charge state.

FIG. 4B shows how a series of pusher pulses (P₁ to P₆) or energisationsof a pusher electrode 10 of a Time of Flight mass analyser 13 may beeffected within or during one cycle of ions being pulsed into an ionmobility spectrometer or separator 4. Six pulses are shown in FIG. 4Bfor ease of illustration only. However, in practice, the pusherelectrode 10 may be energised, for example, several hundred times beforea new pulse of ions is admitted into the ion mobility spectrometer orseparator 4. Ions arriving at the ion detector 12 due to beingorthogonally accelerated by the first pusher pulse P₁ will have aslightly higher ion mobility than the ions subsequently orthogonallyaccelerated by the second pusher pulse P₂. Similarly, ions which areorthogonally accelerated by pusher pulse P_(n) will have a slightlyhigher ion mobility than ions orthogonally accelerated by pusher pulseP_(n+1). Summing all of the mass spectral data due to all the pusherpushes during a single cycle of ions being pulsed into the ion mobilityspectrometer or separator 4 enables an integrated mass spectrum to beproduced which corresponds to ions having all charge states andmobilities. Each individual mass spectrum acquired due to a singlepusher pulse event P_(n) can be considered as relating to a verticalsection or slice through the plot show in FIG. 3B at a particular drifttime T_(n) (where T is defined as the time between ions being pulsedinto the ion mobility spectrometer or separator 4 and the application ofpusher pulse P_(n)).

If the Time of Flight acquisition for a particular pusher pulse P_(n) isconfigured such that experimental data is either only acquired or isonly displayed relating to ions which arrive after a predeterminedflight time, and the predetermined flight time is set so as to lie, forexample, between the singly charged and doubly charged bands or regionsas shown in FIG. 3B, then the resultant mass spectrum will then onlyrelate to multiply charged ions. Mass spectral data relating to singlycharged background ions is either not recorded or alternatively isexcluded from the final mass spectrum which is displayed or otherwisegenerated.

The preferred value for the flight time cut-off may vary (e.g. increase)from pusher pulse P_(n) to pusher pulse P_(n+1). According to anembodiment all the mass spectral data from all the pushes in a singlecycle of ions being pulsed into the ion mobility spectrometer orseparator 4 may, for example, give a resultant integrated mass spectrumrelating only to multiply charged ions. Mass spectral data relating tosingly charged ions may be effectively eliminated or otherwise absentfrom the final mass spectrum.

Ions having specific charge state or range of charge states may beenhanced or alternatively attenuated by using the combination of both alow time of flight cut-off and a high time of flight cut-off. FIG. 5illustrates how, for example, triply charged ions have an even shorterdrift time through an ion mobility spectrometer or separator than doublycharged ions having the same mass to charge ratio. An upper flight timecut-off Q-Q′ may be used in conjunction with a lower flight time cut-offP-P′ so that only mass spectral relating to triply charged ions iseither recorded or is used to generate the final mass spectrum.

According to an embodiment mass spectral data relating to all ions maybe acquired but those ions having flight times below a lower time offlight cut-off for each pusher pulse P_(n) may be discarded or excluded.Summation of all the mass spectral data from all pusher pushes can thenbe arranged to result in an integrated mass spectrum which relates justto multiply charged ions. The mass spectral data obtained may also bepost-processed so as to select parts of each mass spectral data setbetween a lower time of flight cut-off and an upper time of flightcut-off. In this way it is possible to construct a mass spectrumrelating to ions having, for example, just one specific charge state(e.g. doubly charged ions) or range of charge states (e.g. doubly adtriply charged ions). Indeed, according to an embodiment separate massspectra may be constructed or otherwise presented for each separatecharge state.

Another (unillustrated) method of preferentially selecting ions having aspecific charge state in the presence of ions having other charge statesis to separate the ions according to their ion mobility in an ionmobility spectrometer or separator. The ions emerging from the ionmobility spectrometer or separator are then passed to a mass filter. Themass filter may comprise, for example, a quadrupole rod set mass filteror an axial Time of Flight drift region in conjunction with asynchronised pusher electrode. The ions are then mass filtered accordingto their mass to charge ratio by the mass filter. A mass filteringcharacteristic (e.g. low mass to charge ratio cut-off) of the massfilter is progressively varied (e.g. increased) or stepped such thations having a first charge state are onwardly transmitted whereas ionshaving a second different charge state are substantially attenuated bythe mass filter. This allows ions having one or more certain specificcharge states to be physically selected from a mixture of ions havingdiffering charge states whilst ions having undesired charge states arephysically attenuated by the mass filter. Multiply charged ions may bepreferentially selected and onwardly transmitted by the mass filterwhilst singly charged ions may be reduced or substantially attenuated bythe mass filter. Alternatively, ions having two or more multiply chargedstates may, for example, be onwardly transmitted by the mass filter.

The mass filter may be operated as a high pass mass to charge ratiofilter so as to transmit substantially only ions having a mass to chargeratio greater than a minimum mass to charge ratio. In this mode ofoperation multiply charged ions can be preferentially transmittedrelative to singly charged ions i.e. doubly, triply, quadruply and ionshaving five or more charges may be onwardly transmitted by the massfilter whilst singly charged ions may be substantially attenuated by themass filter.

Alternatively, the mass filter may be operated as a band pass mass tocharge ratio filter so as to substantially transmit only ions having amass to charge ratio greater than a minimum mass to charge ratio andless than a maximum mass to charge ratio. In this mode of operationmultiply charged ions of a single charge state (e.g. triply charged) maybe preferentially onwardly transmitted by the mass filter whilst ionshaving other charge states may be substantially attenuated by the massfilter. Alternatively, ions having two or more neighbouring orsequential charge states (e.g. doubly and triply charged ions) may beonwardly transmitted by the mass filter whilst ions having all othercharge states may be substantially attenuated by the mass filter.

The mass filter may be scanned so that, for example, the minimum mass tocharge ratio cut-off or the mass to charge ratio transmission window isprogressively increased during a cycle of ions being pulsed into the ionmobility spectrometer or separator and emerging therefrom. Thetransmitted ions may then, for example, be recorded by a mass analysersuch as an orthogonal acceleration Time of Flight mass analyser.

According to a less preferred arrangement, the mass filter mayalternatively comprise a drift region which is maintained at arelatively low pressure. The drift region may have an axis and aninjection electrode for injecting at least some ions in a directionsubstantially orthogonal to the axis. The injection electrode maycomprise a pusher and/or puller electrode of an orthogonal accelerationTime of Flight mass analyser.

Another arrangement is contemplated wherein a second ion trap ispositioned downstream of an ion mobility spectrometer or separator andupstream of a drift region. The second ion trap is arranged to storeions received from the ion mobility spectrometer or separator and thenperiodically to release ions so that a packet of ions is pulsed into thedrift region. An injection electrode may be arranged to inject ions apredetermined period of time after ions have first been released fromthe second ion trap. The period of time may be set such that only ionshaving a desired mass to charge ratio or ions having mass to chargeratios within a desired range are injected by the injection electrodeinto an orthogonal acceleration Time of Flight mass analyser.

The latter arrangement also provides a mode of operation that offers ameans of increasing sensitivity. Being able to increase the sensitivityis particularly advantageous even if singly charged background ions donot imposes a limit to the detection of analyte ions of interest.

In this mode of operation a first packet of ions may be released fromthe second ion trap and the timing of the orthogonal injection pulse maybe set to a predetermined time delay. Then a second packet of ions maybe released from the second ion trap and the predetermined time delaymay be slightly increased. The process of increasing the time delay maybe repeated a number of times during one cycle of pulsing ions into theion mobility spectrometer or separator. The time delay may be increasedas a function of the mass to charge ratio of the ions arriving at theexit of the ion mobility spectrometer or separator. By appropriateselection of the time delay function, the timing of the orthogonalinjection may be optimised according to the mass to charge ratio of ionswithin each packet released into the drift region thereby optimisingsensitivity.

The resolution or selectivity of an axial time of flight mass filter andthe synchronised orthogonal injection of ions will depend upon thelength of the drift region and the width of the orthogonal accelerationregion. The longer the drift region, and the shorter the width of theorthogonal acceleration region then the greater the resolution orselectivity of the axial time of flight mass filter. However, thegreater the resolution or selectivity of the axial time of flight massfilter the smaller the range of mass to charge ratios of ions which canbe injected into the orthogonal acceleration Time of Flight massanalyser. If this range of mass to charge ratios is smaller than thatpresent in the second ion trap then those outside that range of mass tocharge ratios will be discarded. There can therefore be a conflictbetween the desire to discard as few ions as possible and whilstachieving adequate resolution or selectivity of the axial time of flightmass filter. The more selective the mass filter μs, the more ions arelikely to be discarded, thereby reducing any gain in sensitivity.

FIG. 6 shows a first embodiment of the present invention wherein an ionguide 6 is provided downstream of an ion mobility spectrometer orseparator 4 and which effectively interfaces the ion mobilityspectrometer or separator 4 to an orthogonal acceleration Time of Flightmass analyser 13. A continuous ion source such as an Electrospray ionsource may be provided and which generates a beam of ions 1. The beam ofions 1 is then preferably passed to an ion trap 2 which is preferablyarranged upstream of the ion mobility spectrometer or separator 4. Ionsare preferably pulsed out of the ion trap 2 by the application of anextraction voltage to an ion gate 3 which is preferably located orarranged at the exit of the ion trap 2. The ion gate 3 is alsopreferably arranged upstream of the ion mobility spectrometer orseparator 4. The application of an extraction voltage to the ion gate 3preferably causes a pulse of ions to be ejected out of the ion trap 2and to pass into the ion mobility spectrometer or separator 4.

The ion trap 2 may comprise a quadrupole or other multi-pole rod set.According to a preferred embodiment the ion trap 2 may have a length ofapproximately 75 mm. According to other embodiments the ion trap 2 maycomprise an ion tunnel ion trap comprising a plurality of electrodeshaving apertures through which ions are transmitted in use. Theapertures are preferably all the same size. In other embodiments atleast 60%, 65%, 70%, 75%, 80%, 85%, 90% or 95% of the electrodes of theion trap 2 have apertures which are substantially the same size. The iontrap 2 may according to one embodiment comprise approximately 50electrodes having apertures through which ions are transmitted.

Adjacent electrodes of the ion trap 2 are preferably connected toopposite phases of a two phase AC or RF voltage supply. The applicationof a two phase AC or RF voltage to the electrodes of the ion trap 2preferably causes ions to be radially confined, in use, within the iontrap 2 due to the generation of a radial pseudo-potential well. The ACor RF voltage applied to the electrodes of the ion trap 2 may have afrequency within the range 0.1-3.0 MHz, preferably 0.3-2.0 MHz, furtherpreferably 0.5-1.5 MHz.

In a preferred embodiment the electrodes comprising the ion trap 2 arepreferably maintained at a certain DC voltage V_(rf1) (as shown in FIG.7B). In order to trap ions within the ion trap 2, the ion gate 3arranged downstream of the ion trap 2 is preferably maintained at ahigher DC potential V_(trap) than the DC potential V_(rf1) at which theelectrodes of the ion trap 2 are maintained. Accordingly, ions arepreferably confined axially within the ion trap 2 and are preferablysubstantially prevented from leaving the ion trap 2. The voltage appliedto the ion gate 3 is then preferably periodically dropped to a potentialV_(extract) which is preferably lower than the potential V_(rf1) atwhich the electrodes of the ion trap 2 are otherwise normallymaintained. The potential is only dropped to the relatively lowpotential V_(extract) for a relatively short period of time and thispreferably causes a pulse of ions to be ejected out from the ion trap 2and to be admitted or otherwise pass into the ion mobility spectrometeror separator 4 which is preferably arranged downstream of the ion trap2.

According to an alternative embodiment a pulsed ion source may be usedinstead of a continuous ion source. The pulsed ion source may, forexample, comprise a Matrix Assisted Laser Desorption Ionisation(“MALDI”) ion source or a Laser Desorption Ionisation ion source. If apulsed ion source is used then the ion source may be directly coupled tothe ion mobility spectrometer or separator 4 in which case the ion trap2 and ion gate 3 are not required and hence may be omitted.

The ion mobility spectrometer or separator 4 is preferably arranged suchthat ions which are pulsed into the ion mobility spectrometer orseparator 4 are preferably caused to become temporally separated basedupon or according to their ion mobility. The ion mobility spectrometeror separator 4 may take a number of different forms.

According to one embodiment the ion mobility spectrometer or separator 4may comprise a drift tube having a number of guard rings distributedwithin the drift tube. The guard rings may be interconnected byequivalent valued resistors and connected to a DC voltage source. Alinear or stepped DC voltage gradient may preferably maintained alongthe length of the drift tube. The guard rings are preferably notconnected to an AC or RF voltage source according to this embodiment.

According to another embodiment the ion mobility spectrometer orseparator 4 may comprise a plurality of ring, annular, plate or otherelectrodes. Each electrode preferably has an aperture therein throughwhich ions are preferably transmitted in use. The apertures arepreferably all the same size and are preferably circular. In otherembodiments at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90% or 95%of the electrodes of the ion mobility spectrometer or separator 4 haveapertures which are substantially the same size or area.

According to the preferred embodiment the ion mobility spectrometer orseparator 4 preferably has a length between 100 mm and 200 mm.

The ion mobility spectrometer or separator 4 preferably comprises aplurality of electrodes arranged in a vacuum chamber. The ion mobilityseparator or spectrometer 4 is preferably provided in a vacuum chamberwhich is preferably maintained, in use, at a pressure within the range0.1-10 mbar. According to less preferred embodiments, the vacuum chambermay be maintained at pressures greater than 10 mbar and up to or nearatmospheric pressure. According to other less preferred embodiments, thevacuum chamber may be maintained at pressures below 0.1 mbar.

Alternate or adjacent electrodes of the ion mobility spectrometer orseparator 4 are preferably coupled to opposite phases of a two phase ACor RF voltage supply. The AC or RF voltage supply preferably has afrequency within the range 0.1-3.0 MHz, preferably 0.3-2.0 MHz, furtherpreferably 0.5-1.5 MHz. The two phase AC or RF voltage preferablyapplied to the electrodes of the ion mobility spectrometer or separator4 preferably causes a pseudo-potential well to be generated whichpreferably acts to radially confine ions within the ion mobilityspectrometer or separator 4.

The electrodes comprising the ion trap 2 and the electrodes comprisingthe ion mobility spectrometer or separator 4 may according to oneembodiment be interconnected by resistors to a DC voltage supply whichmay comprise a 400 V supply. The resistors which interconnect theelectrodes of the ion mobility spectrometer or separator 4 may besubstantially equal in value such that a substantially constant orlinear axial DC voltage gradient may be maintained along the length ofthe ion mobility spectrometer or separator 4. FIG. 7B shows a linear DCvoltage gradient being maintained across or along the ion mobilityspectrometer or separator 4 according to this embodiment. However,according to other embodiments the DC voltage gradient maintained alongthe length of the ion mobility spectrometer or separator 4 may beslightly or substantially stepped in profile or may have a differentprofile.

The DC trapping potential or voltage V_(trap) and the extractionpotential or voltage V_(extract) which are preferably applied to the iongate 3 (if provided) may float on the DC voltage supply which ispreferably connected to or applied to the ion mobility spectrometer orseparator 4. The AC or RF voltage supply which is preferably applied tothe electrodes of the ion mobility spectrometer or separator 4 ispreferably isolated from the DC voltage supply by a capacitor.

According to an alternative embodiment, the ion mobility spectrometer orseparator 4 may comprise a plurality of electrodes having aperturesthrough which ions are transmitted in use and wherein one or moretransient DC voltages or one or more transient DC voltage waveforms areapplied to the electrodes. The one or more transient DC voltages or oneor more transient DC voltage waveforms which are preferably applied tothe plurality of electrodes of the ion mobility spectrometer orseparator 4 preferably form one or more potential hills which preferablyhave a relatively low amplitude such that at least some ions may pass orslip over the one or more potential hills as they are being translatedalong the length of the ion mobility spectrometer or separator 4. FIG.7C illustrates this embodiment and shows a plurality of transient DCvoltages having relatively low amplitudes being applied to theelectrodes of the ion mobility spectrometer or separator 4. The one ormore transient DC voltages or one or more transient DC voltage waveformswhich are preferably applied to the electrodes of the ion mobilityspectrometer or separator 4 are preferably progressively applied to asuccession of electrodes forming the ion mobility spectrometer orseparator 4 such that one or more potential hills move along the axis orlength of the ion mobility spectrometer or separator 4 preferablytowards the exit of the ion mobility spectrometer or separator 4.

A buffer gas is preferably maintained within the ion mobilityspectrometer or separator 4 and preferably imposes a viscous drag uponthe movement of ions. The amplitude and average velocity of the one ormore potential hills which are preferably translated along the length ofthe ion mobility spectrometer or separator 4 is preferably set or isotherwise arranged such that at least some ions will slip or pass over apotential hill or barrier as it passes along the length of the ionmobility spectrometer or separator 4. Ions having relatively low ionmobilities are more likely to slip over a potential hill than ionshaving relatively high mobilities. As a result, ions having differention mobilities will be transported at different velocities through andalong the ion mobility spectrometer or separator 4. Ions will thereforebecome substantially separated according to their ion mobility.

Typical drift or transit times of ions through the preferred ionmobility spectrometer or separator 4 are of the order of a severalmilliseconds. After all the ions which were initially pulsed into theion mobility spectrometer or separator 4 have preferably traversed thelength of the ion mobility spectrometer or separator 4, another pulse ofions is preferably admitted or otherwise injected into the ion mobilityspectrometer or separator 4. This marks the start of a new cycle ofoperation. Many cycles of operation may be performed during a singleexperimental run or analysis.

According to the preferred embodiment a particularly preferred aspect ofthe present invention is that an ion guide 6 is provided downstream ofthe ion mobility spectrometer or separator 4. The ion guide 6 may beprovided in a separate vacuum chamber to that in which the ion mobilityspectrometer or separator 4 is provided. Alternatively, the ion guide 6may be provided in the same vacuum chamber as the ion mobilityspectrometer or separator 4. If the ion guide 6 is provided in aseparate vacuum chamber to that of the ion mobility spectrometer orseparator 4 then the two vacuum chambers are preferably separated by adifferential pumping aperture 5 as shown in FIG. 6.

According to the preferred embodiment the ion guide 6 arrangeddownstream of the ion mobility spectrometer or separator 4 preferablycomprises an ion guide comprising a plurality of plate, ring or annularelectrodes having apertures through which ions are transmitted in use.The apertures of the electrodes forming the ion guide 6 are preferablyall the same size. In less preferred embodiments at least 60%, 65%, 70%,75%, 80%, 85%, 90% or 95% of the electrodes forming the ion guide 6 haveapertures which are substantially the same size. Adjacent electrodes ofthe ion guide 6 are preferably connected to the opposite phases of a twophase AC or RF supply.

One or more transient DC voltages or one or more transient DC voltagewaveforms are preferably applied to the plurality of electrodes formingthe ion guide 6. As a result, one or more potential hills or barriers oraxial potential wells are preferably formed in the ion guide 6 and whichare then preferably translated along the length of the ion guide 6. Theone or more transient DC voltages or one or more transient DC voltagewaveforms are preferably progressively applied to a succession ofelectrodes of the ion guide 6 such that one or more potential hills orbarriers or axial potential wells are created which preferably movealong the axis of the ion guide 6 preferably towards the exit of the ionguide 6.

The one or more transient DC voltages or potentials or one or moretransient DC voltage or potential waveforms which are preferably appliedto the electrodes of the ion guide 6 preferably cause a plurality ofaxial potential wells to be created which are then preferably translatedalong the length of the ion guide 6. The one or more transient DCvoltages or potentials or one or more transient DC voltage or potentialwaveforms which are preferably applied to the electrodes of the ionguide 6 preferably cause ions which emerge from the ion mobilityspectrometer or separator 4 and which are received by or into the ionguide 6 to be partitioned or separated into a plurality of separate ordiscrete axial potential wells. The ions in each separate potential wellare then preferably urged along and through the ion guide 6. The axialpotential wells are preferably real potential wells rather thanpseudo-potential wells.

The ion guide 6 is preferably provided in a vacuum chamber or isotherwise preferably maintained, in use, at a pressure within the range10⁻³-10⁻² mbar. The ion guide 6 may preferably be maintained at apressure which is at least on order of magnitude lower than the pressureat which the ion mobility spectrometer or separator 4 is maintained.According to less preferred embodiments the vacuum chamber in which theion guide 6 is housed may be maintained at a pressure greater than 10⁻²mbar up to a pressure at or near 1 mbar. According to less preferredembodiments, the vacuum chamber housing the ion guide 6 mayalternatively be maintained at a pressure below 10⁻³ mbar. The gaspressure in the ion guide 6 is preferably sufficient to imposecollisional damping of ion motion but is preferably not sufficient so asto impose excessive viscous drag upon the movement of ions.

The amplitude and average velocity of the one or more potential hills orbarriers or axial potential wells which are preferably created withinthe ion guide 6 is preferably set such that ions preferably will not beable to substantially slip over a potential hill or barrier or be ableto move or pass from one axial potential well to another. Ions aretherefore preferably trapped within an axial potential well which ispreferably translated along the length of the ion guide 6. The ions arepreferably trapped and translated along the ion guide 6 preferablyregardless of their mass, mass to charge ratio or ion mobility. Thepreferred ion guide 6 therefore preferably has the advantageous effectof preserving the order in which ions are received by the ion guide 6from the upstream ion mobility spectrometer or separator 4 and also ofpreserving the composition of ions as they are received from the ionmobility spectrometer or separator 4. Ions received by the ion guide 6from the ion mobility spectrometer or separator 4 are thereforepreferably partitioned in the ion guide 6 and the partitioning of theions maintains the separation of the ions according to their ionmobility. There is therefore preferably a direct correspondence betweenthe ions trapped in the ion guide 6 and the ions emerging from the exitof the preferred ion mobility spectrometer or separator 4.

The ion guide 6 preferably also acts as an interface between the ionmobility spectrometer or separator 4 which may preferably be maintainedat a relatively high pressure and other components of the massspectrometer such as the downstream mass analyser 13 which arepreferably maintained at substantially lower pressures. The ion guide 6may therefore have the function of maintaining the fidelity of packetsor groups of ions received from the ion mobility spectrometer orseparator 4 and also of communicating these ions from a relatively highpressure region (e.g. the ion mobility spectrometer or separator 4) to arelatively low pressure region (e.g. a mass analyser 13).

According to an embodiment the ion guide 6 preferably transmits ionswithout substantially fragmenting them. However, according toalternative embodiments, ions may be accelerated out of the ion mobilityspectrometer or separator 4 and into the ion guide 6 with sufficientkinetic energy such that the ions are caused to collide with gasmolecules present in the ion guide 6 such that they are caused tofragment into daughter, fragment or product ions. Subsequent massanalysis of the daughter, fragment or product ions enables valuable massspectral information about the parent or precursor ion(s) to beobtained.

The kinetic energy of ions entering the ion guide 6 can be controlled,for example, by setting or controlling the level of a potentialdifference or electric field experienced by the ions emerging from theion mobility spectrometer or separator 4 immediately prior to enteringthe ion guide 6. The level of the potential difference or electric fieldmay preferably be switched near instantaneously. According to anembodiment the level of the potential difference or electric field canbe repeatedly and/or regularly switched between a first level whereinthe potential difference or electric field is relatively high and asecond level wherein the potential difference or electric field isrelatively low. Accordingly, ions may be caused to be fragmented as theyenter the ion guide 6 when the potential difference or electric field isat the first level and wherein the potential difference or electricfield is relatively high. Conversely, ions will not be substantiallyfragmented when the potential difference or electric field is at thesecond level and wherein the potential difference or electric field isrelatively low. Accordingly, the ion guide 6 may therefore effectivelybe switched regularly and repeatedly back and forth between a mode ofoperation wherein parent or precursor ions are transmitted by the ionguide 6 substantially without being fragmented and another mode ofoperation wherein parent or precursor ions are caused to fragment uponentering the ion guide 6.

The voltage or potential difference or electric field experienced by theions prior to entering the ion guide 6 may also be varied (e.g.progressively increased) as ions progressively emerge from the exit ofthe ion mobility spectrometer or separator 4 and preferably before afurther pulse of ions is admitted or otherwise injected into the ionmobility spectrometer or separator 4. The voltage or potentialdifference or electric field may be set such that the kinetic energy ofone or more species of ion emerging from the ion mobility spectrometeror separator 4 is preferably optimised for fragmentation as the ionsenter the ion guide 6. Alternatively, the voltage or potentialdifference or electric field may be progressively varied as ions exitthe ion mobility spectrometer or separator 4 such that the collisionenergy is approximately or substantially optimised for all species ofions as the ions emerge from the exit of the ion mobility spectrometeror separator 4 and enter the ion guide 6.

According to a preferred embodiment transfer optics or an ion opticallens arrangement 8 may optionally be provided preferably in a furthervacuum chamber downstream of the vacuum chamber housing the ion guide 6.The transfer optics or ion optical lens arrangement 8 may comprise anEinzel electrostatic lens. A differential pumping aperture 7 may beprovided between the vacuum chamber housing the ion guide 6 and thevacuum chamber housing the transfer optics or ion optical lensarrangement 8. The transfer optics or ion optical lens arrangement 8 ispreferably arranged to accelerate and guide ions through a furtherdifferential pumping aperture 9 and into a vacuum chamber housing themass analyser 13. The vacuum chamber housing the transfer optics or ionoptical lens arrangement 8 preferably acts as an intermediate region orinterface between the ion guide 6 which may, for example, be maintainedat a relatively intermediate pressure and the mass analyser 13 which ispreferably maintained at a relatively low pressure.

According to a particularly preferred embodiment the mass analyser maycomprise an orthogonal acceleration Time of Flight mass analyser 13comprising a pusher and/or puller electrode 10 for injecting ions intoan orthogonal drift or time of flight region. A reflectron 11 may beprovided for reflecting ions which have traveled through the orthogonaldrift or time of flight region back towards an ion detector 12 which ispreferably arranged in proximity to the pusher and/or puller electrode10.

As is well known in the art, at least some of the ions in a packet ofions pulsed into an orthogonal acceleration Time of Flight mass analyser13 are preferably caused to be orthogonally accelerated into theorthogonal drift or time of flight region. Ions become temporallyseparated as they pass through the orthogonal drift or time of flightregion in a manner which is dependent upon their mass to charge ratio.Ions having a relatively low mass to charge ratio will travel faster inthe drift or time of flight region than ions having a relatively highmass to charge ratio. Ions having a relatively low mass to charge ratiowill therefore reach the ion detector 12 before ions having a relativelyhigh mass to charge ratio. The time taken by an ion to drift through thedrift or time of flight region and to reach the ion detector 12 is usedto determine accurately the mass to charge ratio of the ion in question.The mass to charge ratios of the ions and the number of ions detectedfor each species of ion is preferably used to produce a mass spectrum.

In a conventional mass spectrometer it is known to store ions in an iontrap upstream of an orthogonal acceleration Time of Flight massanalyser. The ions are then non-mass selectively ejected from the iontrap so that all of the ions pass from the ion trap into the massanalyser. The ions in the packet of ions ejected from the ion trap willthen become spatially dispersed by the time that the ions arrive at theorthogonal acceleration region of the mass analyser which is adjacentthe pusher electrode. Accordingly, ions having a relatively low mass tocharge ratio will reach the orthogonal acceleration region adjacent thepusher electrode before ions having a relatively high mass to chargeratio. The pusher electrode is energised so as to orthogonallyaccelerate some ions into the orthogonal acceleration region or driftregion of the Time of Flight mass analyser at a predetermined time afterthe ions have first been released from the ion trap upstream of the massanalyser. Since the time of arrival of an ion at the orthogonalacceleration region adjacent the pusher electrode of the mass analyseris dependent upon the mass to charge ratio of the ion, then appropriatesetting of the time delay between ions being released from the ion trapand ions being orthogonally accelerated ensures that ions having acertain mass to charge ratio will be injected by the pusher electrodeinto the orthogonal acceleration Time of Flight mass analyser with arelatively high sampling duty cycle. However, other ions will eitherhave passed beyond the orthogonal acceleration region adjacent thepusher electrode at the time when the pusher electrode is energised orthey will not yet have reached the orthogonal acceleration regionadjacent the pusher electrode at the time when the pusher electrode isenergised. Accordingly, these ions will not be orthogonally acceleratedinto the orthogonal acceleration drift region and hence these ions willbe lost to the system.

FIG. 8 illustrates in more detail how conventionally the timing of theenergisation of the pusher electrode 10 has the effect of onlyorthogonally accelerating some ions having a specific mass to chargeratio when a group of ions is non-mass selectively pulsed out of an iontrap and into an orthogonal acceleration Time of Flight mass analyser.At an initial time T=0 ions having a wide range of mass to charge ratiosare non-mass selectively released from the ion trap upstream of theorthogonal acceleration Time of Flight mass analyser. After a period oftime Td, ions having a mass to charge ratio M2 will have reached theorthogonal acceleration region adjacent the pusher electrode 10. If thepusher electrode 10 is then energised at this instant, then all of theions having a mass to charge ratio M2 will be injected or will beotherwise orthogonally accelerated into the orthogonal drift or time offlight region of the Time of Flight mass analyser. This will result in asampling duty cycle of substantially 100% for ions having a mass tocharge ratio M2. However, ions having a substantially greater mass tocharge ratio M4 (M4>M2) will not yet have reached the orthogonalacceleration region adjacent the pusher electrode 10 when the pusherelectrode 10 is energised. Accordingly, ions having a mass to chargeratio M4 will not be injected or otherwise be orthogonally acceleratedinto the orthogonal acceleration region of the Time of Flight massanalyser. Similarly, ions having a substantially lower mass to chargeratio M0 (M0<M2) will have already passed the orthogonal accelerationregion adjacent the pusher electrode 10 when the pusher electrode 10 isenergised. Accordingly, ions having a mass to charge ratio M0 will alsonot be injected or otherwise be orthogonally accelerated into theorthogonal acceleration region of the Time of Flight mass analyser. Thesampling duty cycle for ions having a mass to charge ratio of M0 and M4will therefore be 0%.

Ions having intermediate mass to charge ratios M3 and M1 (M2<M3<M4 andM0<M1<M2) will only be partially injected or otherwise orthogonallyaccelerated into the orthogonal drift region of the Time of Flight massanalyser. The duty cycle for ions having a mass to charge ratio of M1and M3 will therefore be somewhere between 0% and 100%.

By adjusting the time delay Td between the time when the pusherelectrode 10 is energised relative to the time when ions are releasedfrom the ion trap into the mass analyser, it is possible to optimise thetransmission and orthogonal acceleration of certain ions having certainmass to charge ratios.

The lower curve in FIG. 9 shows the sampling duty cycle for aconventional mass spectrometer when a continuous beam of ions istransmitted into an orthogonal acceleration Time of Flight massanalyser. The pusher electrode of the mass analyser is repeatedly pulsedto sample the ion beam and the sampling duty cycle is relatively low(0-20%) across the whole of the mass to charge ratio range of interest.FIG. 9 also shows how the sampling duty cycle for ions having a certainmass to charge ratio of M2 can be increased to substantially 100% bypulsing ions into the mass analyser and then setting the time delaybetween the pulsing of ions into the mass analyser and energising thepusher electrode. However, although the sampling duty cycle for ionshaving a mass to charge ratio of M2 is increased, this approach suffersfrom the problem that the sampling duty cycle for other ions havingother mass to charge ratios rapidly tails off to 0%.

The preferred embodiment enables the sampling duty cycle acrosssubstantially the whole mass to charge ratio range of interest to beincreased rather than just enhancing the sampling duty cycle for anarrow range of ions having a narrow range of mass to charge ratios.

The manner of operation of the preferred embodiment of the presentinvention will now be described in more detail with reference to FIG.10. FIG. 10 illustrates an ion guide 6 located downstream of an ionmobility spectrometer or separator and upstream of an orthogonalacceleration Time of Flight mass analyser. One or more transient DCvoltages or one or more transient DC voltage waveforms are preferablyapplied to the electrodes of the ion guide 6 so that one or more axialpotential wells are created in the ion guide 6. The one or more axialpotential wells are then preferably moved or are otherwise translatedfrom the entrance region of the ion guide 6 to the exit region of theion guide 6. Packets of ions are then sequentially ejected from the exitregion of the ion guide 6.

According to the preferred embodiment the timing of the energisation ofthe pusher electrode 10 of the Time of Flight mass analyser arrangeddownstream of the ion guide 6 is preferably set such that all the ionsreleased from an axial potential well which has reached the end of theion guide 6 are then preferably subsequently orthogonally acceleratedinto an orthogonal acceleration or drift region of the mass analyser.

FIG. 10 shows schematically packets or groups of ions being translatedalong the length of the ion guide 6. An exit aperture or region 7 isshown at the exit of the ion guide 6 and which is upstream of anorthogonal acceleration Time of Flight mass analyser comprising a pusherelectrode 10. The centre of the pusher electrode 10 is preferablyarranged at an axial distance L1 from the exit aperture or region 7 ofthe ion guide 6. The pusher electrode 10 preferably has a width Wb.

At a time T=0 a first packet of ions comprising ions contained within anfirst axial potential well which has preferably reached the exit regionof the ion guide 6 is released from the ion guide 6. The ions releasedfrom the first axial potential well preferably all have a mass to chargeratio of substantially M2 and preferably pass towards the pusherelectrode 10. After a period of time Td the ions having a mass to chargeratio M2 will preferably have reached the orthogonal acceleration regionadjacent the centre of the pusher electrode 10. The pusher electrode 10is then preferably energised so that all the ions having a mass tocharge ratio M2 are then preferably injected or are otherwiseorthogonally accelerated into the orthogonal drift region of the Time ofFlight mass analyser 13. The distance L1 between the exit of the ionguide 6 and the centre of the pusher electrode 10 is preferably arrangedso as to be relatively short. The pusher electrode 10 is also preferablyarranged so as to have a suitably wide width Wb such that the spatialspread of ions having a mass to charge ratio M2 when they arrive at theorthogonal acceleration region is preferably smaller than the width Wbof the pusher electrode 10. Accordingly, the sampling duty cycle for theions having a mass to charge ratio M2 is preferably substantially 100%.

At a later time a second packet of ions is then preferably released froma second axial potential well which has preferably now reached the exitregion of the ion guide 6. The ions released from the second axialpotential well preferably have a mass to charge ratio of substantiallyM3 which is preferably at least slightly greater than M2. This isbecause the ions contained in each axial potential well reflect theorder in which ions are received from the ion mobility spectrometer orseparator 4 and the mass to charge ratio of ions emerging from the ionmobility spectrometer or separator 4 preferably increases with time. Theions having a mass to charge ratio M3 are then preferably ejected fromthe ion guide 6 and preferably move towards the pusher electrode 10. Thepusher electrode 10 is then preferably energised after a time delaywhich is preferably slightly greater than Td. This reflects the factthat the ions have a slightly greater mass to charge ratio M3 than theions in the first packet having a mass to charge ratio M2 and willtherefore take slightly longer to reach the orthogonal accelerationregion adjacent pusher electrode 10.

The process is then preferably repeated in a similar manner for a thirdpacket of ions comprising ions having a mass to charge ratio ofsubstantially M5 (wherein M5>M4>M3) which are preferably released from athird axial potential well when that axial potential well preferablyreaches the exit region of the ion guide 6.

Embodiments are contemplated wherein, for example, 200 or more separatepackets of ions may be successively released from separate axialpotential wells which successively reach the end of the ion guide 6during the course of a single cycle of pulsing ions into the ionmobility spectrometer or separator 4. For sake of illustration only, theion mobility spectrometer or separator 4 may have a cycle time of 10 msi.e. ions are pulsed into the ion mobility spectrometer or separator 4and may take up to 10 ms to emerge from the ion mobility spectrometer orseparator 4. The ions emerging from the ion mobility spectrometer orseparator 4 over the period of 10 ms may be arranged to be collected ortrapped in one of 200 successive axial potential wells which arepreferably created in the ion guide 6. Each axial potential well is thenpreferably subsequently translated along the length of the ion guide 6from the entrance region of the ion guide 6 to the exit region of theion guide 6. Each axial potential well formed in the ion guide 6 maytherefore take approximately 50 μs to move or otherwise be translatedfrom the entrance region of the ion guide 6 to the exit region of theion guide 6.

For each packet of ions released from an axial potential well which hasbeen translated from the entrance region to the exit region of the ionguide 6, a corresponding optimum delay time between the release of theions from the ion guide 6 and the energisation of the pusher electrode10 is preferably determined and set. The delay time between the releaseof a packet of ions from the exit of the ion guide 6 and the applicationof an orthogonal acceleration pusher voltage to the pusher electrode 10is preferably progressively increased to reflect the fact that the ionstrapped in the initial axial potential wells created in the ion guide 6will have relatively low mass to charge ratios whereas ions subsequentlyreceived from the ion mobility spectrometer or separator 4 at a latertime and which are trapped in subsequently created axial potential wellswill have relatively high mass to charge ratios.

FIG. 11 shows some experimental results which illustrate the significantenhancement in sampling duty cycle which is obtainable according to thepreferred embodiment. It is to be noted that advantageously anenhancement in sampling duty cycle is obtained over the whole of themass to charge ratio range of interest rather than just over arelatively narrow mass to charge ratio range. The sampling duty cycle asshown in FIG. 11 relates to all doubly charged analyte ions which wereobserved. FIG. 11 also shows for comparison purposes the sampling dutycycle measured when the same sample was analysed by passing a continuousion beam into the mass analyser and repeatedly pulsing the pusherelectrode.

FIG. 12 shows a second embodiment of the present invention. The secondembodiment differs from the first embodiment as described above withreference to FIG. 6 in that the optional ion trap 2 provided upstream ofthe ion mobility spectrometer or separator 4 in the first embodiment ispreferably replaced with a second ion guide 14. The second embodiment isotherwise preferably substantially similar to the first embodiment. Theion mobility spectrometer or separator 4 and the ion guide 6 provideddownstream of the ion mobility spectrometer or separator 4 preferablytake one of the forms as described above in relation to the firstembodiment of the present invention as described with reference to FIG.6. The various different ion sources described above in relation to thefirst embodiment may also be used in relation to the second embodiment.The second ion guide 14 may take the same form as the ion guide 6arranged downstream of the ion mobility spectrometer or separator 4 andas described in reference to the first embodiment.

The second ion guide 14 is preferably provided upstream of the ionmobility spectrometer or separator 4 and preferably comprises aplurality of electrodes having apertures through which ions arepreferably transmitted in use. The apertures of the electrodes formingthe second ion guide 14 are preferably substantially all the same size.In other embodiments at least 60%, 65%, 70%, 75%, 80%, 85%, 90% or 95%of the electrodes of the second ion guide 14 have apertures which aresubstantially the same size. Adjacent electrodes of the second ion guide14 are preferably connected to the opposite phases of a two-phase AC orRF supply.

According to the second embodiment one or more transient DC voltages orpotentials or one or more transient DC voltage or potential waveformsare preferably applied to the electrodes of the second ion guide 14 inorder to form one or more potential hills or barriers. The one or moretransient DC voltages or potentials or one or more transient DC voltageor potential waveforms are preferably progressively applied to asuccession of electrodes of the second ion guide 14 such that one ormore potential hills or barriers move along the axis of the second ionguide 14 towards an exit region of the second ion guide 14.

The second ion guide 14 is preferably provided in a vacuum chamber or isotherwise preferably maintained, in use, at a pressure within the range0.001-0.01 mbar. According to less preferred embodiments, the second ionguide 14 may be maintained at a pressure greater than 0.01 mbar up to apressure at or near 1 mbar. According to less preferred embodiments thesecond ion guide 14 may alternatively be maintained at a pressure below0.001 mbar.

The gas pressure at which the second ion guide 14 is preferablymaintained and is preferably sufficient to impose collisional damping ofion motion but is preferably not sufficient so as to impose excessiveviscous drag upon the movement of ions. The amplitude and averagevelocity of the one or more potential hills or barriers created withinthe second ion guide 14 is preferably set such that ions preferably willnot substantially slip or otherwise move over a potential hill orbarrier. Ions are therefore preferably trapped in one or more axialpotential wells which are preferably translated along the length of thesecond ion guide 14. Ions are preferably trapped and transportedregardless of their mass, mass to charge ratio or ion mobility.

The pressure in the second ion guide 14 may be the same as the pressurein the ion guide 6 arranged downstream of the ion mobility spectrometeror separator 4. In a preferred embodiment the second ion guide 14provided upstream of the ion mobility spectrometer or separator 4 andthe ion guide 6 provided downstream of the ion mobility spectrometer orseparator 4 may be provided in the same vacuum chamber. The intermediateion mobility spectrometer or separator 4 may be contained within aseparate housing positioned within the vacuum chamber containing the ionguide 6 provided downstream of the ion mobility spectrometer orseparator 4 and the second ion guide 14 provided upstream of the ionmobility spectrometer or separator 4. A collision gas, preferablynitrogen or argon, may be supplied to the housing containing the ionmobility spectrometer or separator 4 in order to maintain the ionmobility spectrometer or separator 4 at a relatively high pressure. Thehousing containing the ion mobility spectrometer or separator 4 may bemaintained, for example, at a pressure between 0.1 and 10 mbar. Thecollision gas present in the housing containing the ion mobilityspectrometer or separator 4 may be allowed to leak into the vacuumchamber containing the second ion guide 14 and the ion guide 6 arrangeddownstream of the ion mobility spectrometer or separator 4 through anentrance and exit aperture in the housing as shown schematically in FIG.7A. The vacuum chamber containing the housing is preferably pumped suchas to maintain the pressure in the vacuum chamber within the range 0.001and 0.01 mbar.

Ions may be transported in and along the second ion guide 14 and maypreferably be released as packets of ions into or towards the ionmobility spectrometer or separator 4 which is preferably arrangeddownstream of the second ion guide 14. The cycle time of the second ionguide 14 (i.e. the time taken for an axial potential well to betranslated along the length of the second ion guide 14) may preferablybe equal to or substantially similar to the cycle time of the ionmobility spectrometer or separator 4. Alternatively, ions may beaccumulated and held in an ion trapping region provided preferably nearthe exit of the second ion guide 14. The ions may then be released fromthe second ion guide 14 into or towards the ion mobility spectrometer orseparator 4 at the start of each cycle of the ion mobility spectrometeror separator 4. In this mode of operation the cycle time of translatingaxial potential wells along the length of the second ion guide 14 thesecond ion guide 14 does not need to be match the cycle time of the ionmobility spectrometer or separator 4.

In one mode of operation ions may be arranged such that they aresufficiently energetic when they enter the second ion guide 14 that theycollide with gas molecules present in the second ion guide 14 and arecaused to fragment into daughter, fragment or product ions. Thedaughter, fragment or product ions may then be passed or onwardlytransmitted to the ion mobility spectrometer or separator 4. Thedaughter, fragment or product ions may then be subsequently separatedaccording to their ion mobility in the ion mobility separator orspectrometer 4. The daughter, fragment or product ions may thenpreferably be ejected from or otherwise emerge from the ion mobilityspectrometer or separator 4 and are preferably received and trapped in aplurality of axial potential wells generated in the ion guide 6 which ispreferably located downstream of the ion mobility spectrometer orseparator 4. Packets of ions are then preferably ejected from the ionguide 6 and are preferably subsequently mass analysed by the orthogonalacceleration Time of Flight mass spectrometer 13.

The energy of ions entering the second ion guide 14 may be controlled,for example, by setting the level of a voltage or potential differenceor electric field experienced by the ions prior to entering the secondion guide 14. Since the voltage or potential difference or electricfield can be switched near instantaneously, the second ion guide 14 canbe regularly and repeatedly switched between a relatively highfragmentation mode of operation and a relatively low fragmentation modeof operation.

The voltage or potential difference or electric field experienced by theions prior to entering the second ion guide 14 may also be switchedalternately between a relatively low level and a relatively high levelupon successive cycles of pulsing ions into the ion mobilityspectrometer or separator 4.

In yet another mode of operation daughter, fragment or product ionsemerging from the ion mobility spectrometer or separator 4 may bearranged such that they are sufficiently energetic that when they enterthe ion guide 6 arranged downstream of the ion mobility spectrometer orseparator 4 they themselves are then caused to collide with gasmolecules present in the ion guide 6 and are caused to further fragmentinto grand-daughter or second generation fragment ions. Subsequent massanalysis of the grand-daughter or second generation fragment ions yieldsvaluable information about the related parent and/or daughter ion(s).

The energy of ions entering the ion guide 6 downstream of the ionmobility spectrometer or separator 4 can be controlled, for example, bysetting the level of a voltage or potential difference or electric fieldexperienced by the ions prior to entering the ion guide 6. Since thevoltage or potential difference or electric field can be switched nearinstantaneously, the ion guide 6 can be repeatedly and regularlyswitched between a first mode wherein parent or daughter ions arefragmented and a second mode wherein parent or daughter ions are notsubstantially fragmented.

The voltage or potential difference or electric field experienced by theions prior to entering the ion guide 6 arranged downstream of the ionmobility spectrometer or separator 4 may also be varied as ionsprogressively emerge from the ion mobility spectrometer or separator 4.The voltage or potential difference or the electric field may be setsuch that the collision energy is optimised for one or more species ofparent or daughter ions as ions emerge from the ion mobilityspectrometer or separator 4. Alternatively, the voltage or potentialdifference or the electric field may be progressively varied (e.g.increased) as ions emerge from the ion mobility spectrometer orseparator 4 such that the collision energy is approximately optimisedfor all species of parent or daughter ions as ions emerge from the ionmobility spectrometer or separator 4.

The voltage or potential difference or electric field experienced by theparent or daughter ions prior to entering the ion guide 6 arrangeddownstream of the ion mobility spectrometer or separator 4 may also beswitched alternately between a relatively low level and a relativelyhigh level upon successive cycles of ions being pulsed into the ionmobility spectrometer or separator 4.

Some experimental results are shown in FIGS. 13A and 13B. FIG. 13A showsa mass spectrum of a peptide mixture which has been mass analysed in aconventional manner. The sampling duty cycle was not enhanced and themass spectral data was not post-processed in order to produce a massspectrum relating just to ions having a particular charge state. FIG.13B shows a comparable mass spectrum wherein the sampling duty cycle wasenhanced according to the preferred embodiment. As can be seen fromcomparing FIGS. 13A and 13B, the preferred approach to enhancing thesampling duty cycle according to the preferred embodiment resulted inthe sensitivity being increased by a factor of approximately ×6 acrossthe whole mass to charge ratio range of interest. As can be seen fromFIG. 13B, the preferred embodiment enables a significant improvement inthe art to be achieved.

FIGS. 14A-C show a small portion of the mass spectrum shown in FIGS. 13Aand 13B in greater detail across the mass to charge ratio range 658-680.FIG. 14A shows a portion of the mass spectrum obtained in a conventionalmanner. FIG. 14B shows a corresponding mass spectrum obtained byenhancing the sampling duty cycle according to the preferred embodiment.FIG. 14C shows an additional increase or improvement in the signal tonoise ratio obtained by further post-processing the mass spectral datawhich was acquired in order to remove mass spectral data relating tosingly charged background ions. This was achieved by exploiting therelationship between the mass to charge ratio of ions and their drifttime through the ion mobility spectrometer or separator which dependsupon the charge state of the ions.

FIGS. 15A-C show another small portion of the mass spectrum shown inFIGS. 13A and 13B in greater detail across the mass to charge ratiorange 780-795. FIG. 15A shows a portion of the mass spectrum obtained ina conventional manner. FIG. 15B shows a corresponding mass spectrumobtained by enhancing the sampling duty cycle according to the preferredembodiment. FIG. 15C shows an additional increase or improvement in thesignal to noise ratio obtained by further post-processing the massspectral data to remove mass spectral data relating to singly chargedbackground ions. This was achieved by exploiting the relationshipbetween the mass to charge ratio of ions and their drift times throughan ion mobility spectrometer or separator which depends upon the chargestate of the ions.

According to a particularly preferred embodiment an Atmospheric PressureIonisation ion source may be provided. A relatively high pressure (e.g.>10⁻³ mbar) ion guide may be arranged to receive ions from the ionsource. The ion guide preferably comprises a plurality of electrodeshaving apertures through which ions are transmitted in use. One or moretransient DC voltages or potentials or one or more transient DC voltageor potential waveforms are preferably applied to the electrodes of theion guide. A relatively low pressure (e.g. <10⁻³ mbar) quadrupole rodset mass filter is preferably arranged downstream of the ion guide.

A further ion guide is preferably arranged downstream of the mass filterand preferably comprises a plurality of electrodes having aperturesthrough which ions are transmitted in use. One or more transient DCvoltages or potentials or one or more transient DC voltage or potentialwaveforms are preferably applied to the electrodes of the further ionguide. The further ion guide is preferably maintained at a relativelyhigh pressure (e.g. >10⁻³ mbar) and ions may be fragmented and/ortrapped within the further ion guide.

An ion mobility spectrometer or separator is preferably arrangeddownstream of the further ion guide and ions are preferably pulsed outof the further ion guide into the ion mobility spectrometer orseparator. The ion mobility spectrometer or separator preferablycomprises a plurality of electrodes having apertures through which ionsare transmitted in use. One or more transient DC voltages or potentialshaving a relatively low amplitude or one or more transient DC voltage orpotential waveforms having a relatively low amplitude are preferablyapplied to the electrodes of the ion mobility spectrometer or separatorin order to separate ions according to their ion mobility. The ionmobility spectrometer or separator is preferably maintained at apressure >10⁻² mbar.

A yet further ion guide is preferably arranged downstream of the ionmobility spectrometer or separator in order to receive ions emergingfrom the ion mobility spectrometer or separator. The yet further ionguide preferably comprises a plurality of electrodes having aperturesthrough which ions are transmitted in use. One or more transient DCvoltages or potentials or one or more transient DC voltage or potentialwaveforms are preferably applied to the electrodes of the yet furtherion guide. The yet further ion guide preferably maintains the fidelityand/or composition of the packets of ions which preferably emerge fromthe ion mobility spectrometer or separator.

A transfer optic is preferably arranged downstream of the yet furtherion guide and preferably comprises an Einzel or other electrostatic lensarrangement. The transfer optic is preferably maintained at a relativelylow or intermediate pressure (i.e. <10⁻³ mbar) and preferably acts as adifferential pressure pumping stage. An orthogonal acceleration Time ofFlight mass analyser is preferably arranged downstream of the transferoptic and/or the yet further ion guide.

Although according to the preferred embodiment the AC or RF voltageapplied to the electrodes of the ion mobility spectrometer or separator4, the ion guide 6 downstream of the ion mobility spectrometer orseparator and optionally the second ion guide 14 preferably has asinusoidal waveform, other less preferred embodiments are contemplatedwherein the AC or RF voltage supplied or applied to electrode(s) of theion mobility spectrometer or separator 4 and/or the ion guide 6downstream of the ion mobility spectrometer or separator 4 and/or thesecond ion guide 14 may be non-sinusoidal. For example, the AC or RFvoltage may take the form of a square wave.

Although the present invention has been described with reference topreferred embodiments, it will be understood by those skilled in the artthat various changes in form and detail may be made without departingfrom the scope of the invention as set forth in the accompanying claims.

The invention claimed is:
 1. A mass spectrometer comprising: an ionmobility separator wherein an upstream ion funnel is located upstream ofsaid ion mobility separator, the upstream ion funnel comprising aplurality of electrodes having apertures through which ions aretransmitted in use, wherein the apertures of the electrodes of theupstream ion funnel become progressively smaller in size or area,wherein said ion mobility separator comprises a plurality of axialsegments and wherein one or more voltages are applied to the pluralityof axial segments such that ions are partitioned into separate axialregions; a downstream ion funnel arranged downstream of said ionmobility separator, the downstream ion funnel comprising a plurality ofelectrodes having apertures through which ions are transmitted in use,wherein the apertures of the electrodes of the downstream ion funnelbecome progressively smaller in size or area; a mass filter disposeddownstream of the ion mobility separator; and a mass analyser disposeddownstream of the downstream ion funnel, wherein said mass analysercomprises an orthogonal Time of Flight mass analyser, wherein the massspectrometer is configured such that a transit time between the upstreamion funnel and the downstream ion funnel of at least some ions isgreater than 30 ms, and wherein said mass filter is operative toprogressively vary, increase or step a mass filtering characteristic ofsaid mass filter during a cycle of ions emerging from the ion mobilityseparator.
 2. A mass spectrometer as claimed in claim 1, comprising anion trap or trapping region from which ions are periodically releasedfor analysis.
 3. A mass spectrometer as claimed in claim 1, wherein saidmass filter is arranged so that ions having a first charge state areonwardly transmitted whereas ions having a second different charge stateare substantially attenuated by said mass filter.
 4. A mass spectrometeras claimed in claim 1, wherein ions are caused to separate in said ionmobility separator by an electric field and a buffer gas.
 5. A massspectrometer as claimed in claim 1, further comprising DC voltage meansfor maintaining a substantially constant DC voltage gradient along atleast a portion of said ion mobility separator.
 6. A mass spectrometeras claimed in claim 1, wherein said ion mobility separator comprises astack or array of planar, plate or mesh electrodes having aperturesthrough which ions are transmitted in use.
 7. A mass spectrometer asclaimed in claim 1, the mass filtering characteristic comprising a lowmass to charge ratio cut-off.
 8. A mass spectrometer as claimed in claim1, further comprising an electrospray ionisation ion source.
 9. A massspectrometer as claimed in claim 1, further comprising a control systemarranged and adapted to switch the mass spectrometer between a highfragmentation mode of operation and a low fragmentation mode ofoperation at least once every 500 ms.
 10. A mass spectrometer as claimedin claim 9, wherein the control system is arranged and adapted to switchthe mass spectrometer between the high fragmentation mode of operationand the low fragmentation mode of operation at least once every 1 s. 11.A mass spectrometer as claimed in claim 1, comprising means for pulsingions into the ion mobility separator at a rate of greater than onceevery 50 ms.
 12. A mass spectrometer as claimed in claim 1, wherein atransit time through the ion mobility separator of singly charged ionshaving a mass to charge ratio in the range 0 to 200 is greater than 30ms.
 13. A mass spectrometer comprising: an ion mobility separator; anupstream ion funnel located upstream of said ion mobility separator, adownstream ion funnel arranged downstream of said ion mobilityseparator; a mass filter disposed downstream of the ion mobilityseparator, wherein said mass filter is arranged so that ions having afirst charge state are onwardly transmitted whereas ions having a seconddifferent charge state are substantially attenuated by said mass filter;and a mass analyser disposed downstream of the downstream ion funnel,wherein said mass analyser comprises an orthogonal Time of Flight massanalyser, wherein the mass spectrometer is configured such that atransit time of at least some ions between the upstream ion funnel andthe downstream ion funnel is greater than 30 ms, and wherein said massfilter is operative to progressively vary, increase or step a massfiltering characteristic of said mass filter during a cycle of ionsemerging from the ion mobility separator.
 14. A mass spectrometer asclaimed in claim 13, comprising an ion trap or trapping region fromwhich ions are periodically released for analysis.
 15. A massspectrometer as claimed in claim 13, wherein ions are caused to separatein said ion mobility separator by an electric field and a buffer gas.16. A mass spectrometer as claimed in claim 13, further comprising DCvoltage means for maintaining a substantially constant DC voltagegradient along at least a portion of said ion mobility separator.
 17. Amass spectrometer as claimed in claim 13, wherein said ion mobilityseparator comprises a stack or array of planar, plate or meshelectrodes.
 18. A mass spectrometer as claimed in claim 13, the massfiltering characteristic comprising a low mass to charge ratio cut-off.19. A mass spectrometer as claimed in claim 13, further comprising anelectrospray ionisation ion source.
 20. A mass spectrometer as claimedin claim 13, wherein a transit time through the ion mobility separatorof singly charged ions having a mass to charge ratio in the range 0 to200 is greater than 30 ms.